Alignments for a candidate for carB in Archaeoglobus veneficus SNP6

GapMind for Amino acid biosynthesis

Alignments for a candidate for carB in Archaeoglobus veneficus SNP6

Align Carbamoyl-phosphate synthase large chain, chloroplastic; Carbamoyl-phosphate synthetase ammonia chain; Protein VENOSA 3; EC 6.3.5.5 (characterized)
to candidate WP_013684200.1 ARCVE_RS07635 carbamoyl-phosphate synthase large subunit

Query= SwissProt::Q42601
         (1187 letters)



>NCBI__GCF_000194625.1:WP_013684200.1
          Length = 1076

 Score = 1266 bits (3275), Expect = 0.0
 Identities = 649/1089 (59%), Positives = 828/1089 (76%), Gaps = 22/1089 (2%)

Query: 94   KRTDLKKIMILGAGPIVIGQACEFDYSGTQACKALREEGYEVILINSNPATIMTDPETAN 153
            KR D+KKIM++G+GPIVIGQA EFDYSG+QACKALREEGYEV+L+NSNPATIMTDPE A+
Sbjct: 3    KREDIKKIMVIGSGPIVIGQAAEFDYSGSQACKALREEGYEVVLVNSNPATIMTDPEMAD 62

Query: 154  RTYIAPMTPELVEQVIEKERPDALLPTMGGQTALNLAVALAESGALEKYGVELIGAKLGA 213
            RTYI P+T ++V ++IE+E PDALLPT+GGQTALN+AV L E G L+KYGVELIGAKL A
Sbjct: 63   RTYIEPLTADVVARIIERETPDALLPTLGGQTALNIAVQLGEMGVLDKYGVELIGAKLDA 122

Query: 214  IKKAEDRELFKDAMKNIGLKTPPSGIGTTLDECFDIAEKIGEFPLIIRPAFTLGGTGGGI 273
            IKKAEDRELFK+ M  IGL+ P S I   + E   IAE+IG +P+++RPAFTLGGTGGGI
Sbjct: 123  IKKAEDRELFKECMHRIGLEVPRSDIANDISEALSIAEEIG-YPVVVRPAFTLGGTGGGI 181

Query: 274  AYNKEEFESICKSGLAASATSQVLVEKSLLGWKEYELEVMRDLADNVVIICSIENIDPMG 333
            AYN+EE + I   GL  S  +QVL+E+ ++GWKE+ELEVMRDLADNVVIICSIEN DPMG
Sbjct: 182  AYNREELKEIAAHGLEMSMINQVLIEEGVIGWKEFELEVMRDLADNVVIICSIENFDPMG 241

Query: 334  VHTGDSITVAPAQTLTDREYQRLRDYSIAIIREIGVECGGSNVQFAVNPVDGEVMIIEMN 393
            VHTGDSITVAPAQTLTD EYQRLRD +I IIREIGVE GGSN+QFAV+P     + IEMN
Sbjct: 242  VHTGDSITVAPAQTLTDWEYQRLRDAAIDIIREIGVETGGSNIQFAVHPTTERFVAIEMN 301

Query: 394  PRVSRSSALASKATGFPIAKMAAKLSVGYTLDQIPNDITRKTPASFEPSIDYVVTKIPRF 453
            PRVSRSSALASKATGFPIAK+AAKL+VGYTLD+IPNDIT++TPASFEP+IDYVV KIPRF
Sbjct: 302  PRVSRSSALASKATGFPIAKIAAKLAVGYTLDEIPNDITKETPASFEPTIDYVVVKIPRF 361

Query: 454  AFEKFPGSQPLLTTQMKSVGESMALGRTFQESFQKALRSLECGFSGWGCAKIKELDWDWD 513
            AF+KFP + P+L +QMKSVGE MA+GRTF+E+ QKALRSLE G  G G +  K+ D   +
Sbjct: 362  AFDKFPTADPVLGSQMKSVGEVMAIGRTFEEALQKALRSLEIGRYGLG-SDGKDKDVTRE 420

Query: 514  QLKYSLRVPNPDRIHAIYAAMKKGMKIDEIYELSMVDKWFLTQLKELVDVEQYL----MS 569
            ++   LR PN  R+  I  A++KG  ++EIYE++ +D WF+ ++K +V++E+ L      
Sbjct: 421  EIIRKLRYPNAQRVFYIRYALQKGFSVEEIYEITKIDPWFIEKIKNIVEMEKELKELASK 480

Query: 570  GTLSEITKEDLYEVKKRGFSDKQIAFATKTTEEEVRTKRISLGVVPSYKRVDTCAAEFEA 629
             ++ ++  E L + KK GFSD Q+A     +E E+R  R   G+   +K VDTCAAEFEA
Sbjct: 481  HSIDDVPPEILKKAKKLGFSDVQLAKIFGVSEVEIRRIRKRDGISAVFKMVDTCAAEFEA 540

Query: 630  HTPYMYSSYDVECESAPNNKKKVLILGGGPNRIGQGIEFDYCCCHTSFALQDAGYETIML 689
             TPY YS+Y+ E ++ P  K KV+ILGGGPNRIGQGIEFDYCCCH  F+L++ GYETIM+
Sbjct: 541  KTPYYYSTYEEENDAKPTEKPKVMILGGGPNRIGQGIEFDYCCCHAVFSLKEEGYETIMV 600

Query: 690  NSNPETVSTDYDTSDRLYFEPLTIEDVLNVIDLEKPDGIIVQFGGQTPLKLALPIKHYLD 749
            N+NPETVSTDYDTSDRLYFEP+T EDV+N+ + EKP+G+IVQFGGQTPL +A  ++    
Sbjct: 601  NNNPETVSTDYDTSDRLYFEPITHEDVMNIYENEKPEGVIVQFGGQTPLNIAKQLES--- 657

Query: 750  KHMPMSLSGAGPVRIWGTSPDSIDAAEDRERFNAILDELKIEQPKGGIAKSEADALAIAK 809
                   SGA   +I GTS DSID AEDRERF  + + L I QP+ GIA S  +A  IA 
Sbjct: 658  -------SGA---KILGTSVDSIDIAEDRERFAELCNRLGIPQPENGIAHSIEEAKEIAA 707

Query: 810  EVGYPVVVRPSYVLGGRAMEIVYDDSRLITYLENAVQVDPERPVLVDKYLSDAIEIDVDT 869
             +GYPV+VRPSYVLGGRAMEIVYD+  L  Y+  A++V PE+P+L+DK+L DAIE++VD 
Sbjct: 708  RIGYPVLVRPSYVLGGRAMEIVYDEETLERYISEALEVSPEKPILIDKFLEDAIEVEVDA 767

Query: 870  LTDSYGNVVIGGIMEHIEQAGVHSGDSACMLPTQTIPASCLQTIRTWTTKLAKKLNVCGL 929
            L D    VVIGGIMEHIE+AGVHSGDSAC+LP  ++    +  I  +T K+A +LNV GL
Sbjct: 768  LCDG-EEVVIGGIMEHIEEAGVHSGDSACVLPPVSLSQDIIDRIVDYTRKMALELNVVGL 826

Query: 930  MNCQYAITTSGDVFLLEANPRASRTVPFVSKAIGHPLAKYAALVMSGKSLKDLNFEKEVI 989
            +N QYA+     V++LEANPRASRTVPFVSKA G PLAK AA +M+GK LK+L  ++ + 
Sbjct: 827  INIQYAV-KDNIVYVLEANPRASRTVPFVSKATGIPLAKIAAKLMTGKKLKELGVKERLN 885

Query: 990  PKHVSVKEAVFPFEKFQGCDVILGPEMRSTGEVMSISSEFSSAFAMAQIAAGQKLPLSGT 1049
             KHV+VKEAVFPF K  G D +LGPEM+STGEVM I  +F  A+  A++AAG +LP  GT
Sbjct: 886  LKHVAVKEAVFPFIKLPGVDPVLGPEMKSTGEVMGIDYDFGVAYYKAELAAGMRLPTEGT 945

Query: 1050 VFLSLNDMTKPHLEKIAVSFLELGFKIVATSGTAHFLELKGIPVERVLKLHEGRPHAADM 1109
            VF+S+    +  +  +A    ELGFKI+AT+GTA+FL   GI  E V K+ +GRP+  D+
Sbjct: 946  VFISVKKEDRERVLPVAKKLAELGFKIIATNGTANFLRANGIDAEIVNKVSQGRPNILDV 1005

Query: 1110 VANGQIHLMLITSSGDALDQKDGRQLRQMALAYKVPVITTVAGALATAEGIKSLKSSAIK 1169
            + N Q+ L++ T SG    + +G  +R+ A+ + +P ITTV+GA+A  +GI+++K++ + 
Sbjct: 1006 IINRQVDLIINTPSGKR-GKTEGYMIRRAAVDHNIPYITTVSGAIAAVKGIEAIKNAQMT 1064

Query: 1170 MTALQDFFE 1178
            + ++Q++ E
Sbjct: 1065 IKSIQEYHE 1073



 Score =  251 bits (642), Expect = 2e-70
 Identities = 151/403 (37%), Positives = 226/403 (56%), Gaps = 19/403 (4%)

Query: 87  FSPEIVGKRTDLKKIMILGAGPIVIGQACEFDYSGTQACKALREEGYEVILINSNPATIM 146
           +  E   K T+  K+MILG GP  IGQ  EFDY    A  +L+EEGYE I++N+NP T+ 
Sbjct: 549 YEEENDAKPTEKPKVMILGGGPNRIGQGIEFDYCCCHAVFSLKEEGYETIMVNNNPETVS 608

Query: 147 TDPETANRTYIAPMTPELVEQVIEKERPDALLPTMGGQTALNLAVALAESGALEKYGVEL 206
           TD +T++R Y  P+T E V  + E E+P+ ++   GGQT LN+A  L  SGA      ++
Sbjct: 609 TDYDTSDRLYFEPITHEDVMNIYENEKPEGVIVQFGGQTPLNIAKQLESSGA------KI 662

Query: 207 IGAKLGAIKKAEDRELFKDAMKNIGLKTPPSGIGTTLDECFDIAEKIGEFPLIIRPAFTL 266
           +G  + +I  AEDRE F +    +G+  P +GI  +++E  +IA +IG +P+++RP++ L
Sbjct: 663 LGTSVDSIDIAEDRERFAELCNRLGIPQPENGIAHSIEEAKEIAARIG-YPVLVRPSYVL 721

Query: 267 GGTGGGIAYNKEEFESICKSGLAASATSQVLVEKSLLGWKEYELEVMRDLADNVVIICSI 326
           GG    I Y++E  E      L  S    +L++K L    E E++ + D  + VVI   +
Sbjct: 722 GGRAMEIVYDEETLERYISEALEVSPEKPILIDKFLEDAIEVEVDALCD-GEEVVIGGIM 780

Query: 327 ENIDPMGVHTGDSITVAPAQTLTDREYQRLRDYSIAIIREIGVECGGSNVQFAVNPVDGE 386
           E+I+  GVH+GDS  V P  +L+     R+ DY+  +  E+ V  G  N+Q+AV   D  
Sbjct: 781 EHIEEAGVHSGDSACVLPPVSLSQDIIDRIVDYTRKMALELNV-VGLINIQYAVK--DNI 837

Query: 387 VMIIEMNPRVSRSSALASKATGFPIAKMAAKLSVGYTLDQIPNDITRKTPASFEPSIDYV 446
           V ++E NPR SR+    SKATG P+AK+AAKL  G  L ++              ++ +V
Sbjct: 838 VYVLEANPRASRTVPFVSKATGIPLAKIAAKLMTGKKLKEL--------GVKERLNLKHV 889

Query: 447 VTKIPRFAFEKFPGSQPLLTTQMKSVGESMALGRTFQESFQKA 489
             K   F F K PG  P+L  +MKS GE M +   F  ++ KA
Sbjct: 890 AVKEAVFPFIKLPGVDPVLGPEMKSTGEVMGIDYDFGVAYYKA 932


Lambda     K      H
   0.317    0.133    0.383 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 3168
Number of extensions: 149
Number of successful extensions: 18
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 1187
Length of database: 1076
Length adjustment: 46
Effective length of query: 1141
Effective length of database: 1030
Effective search space:  1175230
Effective search space used:  1175230
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.9 bits)

Align candidate WP_013684200.1 ARCVE_RS07635 (carbamoyl-phosphate synthase large subunit)
to HMM TIGR01369 (carB: carbamoyl-phosphate synthase, large subunit (EC 6.3.5.5))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR01369.hmm
# target sequence database:        /tmp/gapView.4180930.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01369  [M=1052]
Accession:   TIGR01369
Description: CPSaseII_lrg: carbamoyl-phosphate synthase, large subunit
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
          0 1668.2   2.0          0 1668.0   2.0    1.0  1  NCBI__GCF_000194625.1:WP_013684200.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000194625.1:WP_013684200.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1668.0   2.0         0         0       1    1050 [.       2    1053 ..       2    1055 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1668.0 bits;  conditional E-value: 0
                             TIGR01369    1 pkredikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePltve 71  
                                            pkredikk++viGsGpivigqAaEFDYsGsqa+kal+eeg+evvLvnsn+At+mtd+e+ad++YiePlt+ 
  NCBI__GCF_000194625.1:WP_013684200.1    2 PKREDIKKIMVIGSGPIVIGQAAEFDYSGSQACKALREEGYEVVLVNSNPATIMTDPEMADRTYIEPLTAD 72  
                                            689******************************************************************** PP

                             TIGR01369   72 avekiiekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealkeineev 142 
                                            +v++iie+E pDa+l+tlGGqtaLn+av+l e+GvL+kygv+l+G+k++aikkaedRe+Fke ++ i++ev
  NCBI__GCF_000194625.1:WP_013684200.1   73 VVARIIERETPDALLPTLGGQTALNIAVQLGEMGVLDKYGVELIGAKLDAIKKAEDRELFKECMHRIGLEV 143 
                                            *********************************************************************** PP

                             TIGR01369  143 akseivesveealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikqvlvekslagwk 213 
                                            ++s+i+++++eal++aeeigyPv+vR+aftlgGtG+gia+n+eelke+++++l++s+i+qvl+e+ + gwk
  NCBI__GCF_000194625.1:WP_013684200.1  144 PRSDIANDISEALSIAEEIGYPVVVRPAFTLGGTGGGIAYNREELKEIAAHGLEMSMINQVLIEEGVIGWK 214 
                                            *********************************************************************** PP

                             TIGR01369  214 EiEyEvvRDskdnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslkiirelgvege.cnvq 283 
                                            E+E+Ev+RD +dn++i+c+iEn+Dp+GvHtGdsi+vaP+qtLtd eyq+lRda++ iire+gve++ +n+q
  NCBI__GCF_000194625.1:WP_013684200.1  215 EFELEVMRDLADNVVIICSIENFDPMGVHTGDSITVAPAQTLTDWEYQRLRDAAIDIIREIGVETGgSNIQ 285 
                                            ****************************************************************988**** PP

                             TIGR01369  284 faldPeskryvviEvnpRvsRssALAskAtGyPiAkvaaklavGysLdelkndvtketvAsfEPslDYvvv 354 
                                            fa++P+++r+v iE+npRvsRssALAskAtG+PiAk+aaklavGy+Lde++nd+tket+AsfEP++DYvvv
  NCBI__GCF_000194625.1:WP_013684200.1  286 FAVHPTTERFVAIEMNPRVSRSSALASKATGFPIAKIAAKLAVGYTLDEIPNDITKETPASFEPTIDYVVV 356 
                                            *********************************************************************** PP

                             TIGR01369  355 kiPrwdldkfekvdrklgtqmksvGEvmaigrtfeealqkalrsleekllglklk.ekeaesdeeleealk 424 
                                            kiPr+++dkf ++d  lg+qmksvGEvmaigrtfeealqkalrsle++ +gl ++ +++ +++ee+ ++l+
  NCBI__GCF_000194625.1:WP_013684200.1  357 KIPRFAFDKFPTADPVLGSQMKSVGEVMAIGRTFEEALQKALRSLEIGRYGLGSDgKDKDVTREEIIRKLR 427 
                                            **************************************************954431456677888899*** PP

                             TIGR01369  425 kpndrRlfaiaealrrgvsveevyeltkidrffleklkklvelekeleee....klkelkkellkkakklG 491 
                                            +pn++R+f+i  al++g+svee+ye+tkid +f+ek+k++ve+ekel+e     ++++++ e lkkakklG
  NCBI__GCF_000194625.1:WP_013684200.1  428 YPNAQRVFYIRYALQKGFSVEEIYEITKIDPWFIEKIKNIVEMEKELKELaskhSIDDVPPEILKKAKKLG 498 
                                            ***********************************************987443356699************ PP

                             TIGR01369  492 fsdeqiaklvkvseaevrklrkelgivpvvkrvDtvaaEfeaktpYlYstyeeekddvevtekkkvlvlGs 562 
                                            fsd q+ak+++vse e+r++rk+ gi  v+k+vDt+aaEfeaktpY+Ystyeee +d++ tek kv++lG+
  NCBI__GCF_000194625.1:WP_013684200.1  499 FSDVQLAKIFGVSEVEIRRIRKRDGISAVFKMVDTCAAEFEAKTPYYYSTYEEE-NDAKPTEKPKVMILGG 568 
                                            ******************************************************.999999999******* PP

                             TIGR01369  563 GpiRigqgvEFDycavhavlalreagyktilinynPEtvstDydiadrLyFeeltvedvldiiekekvegv 633 
                                            Gp+Rigqg+EFDyc+ hav +l+e+gy+ti++n+nPEtvstDyd++drLyFe++t+edv++i+e+ek+egv
  NCBI__GCF_000194625.1:WP_013684200.1  569 GPNRIGQGIEFDYCCCHAVFSLKEEGYETIMVNNNPETVSTDYDTSDRLYFEPITHEDVMNIYENEKPEGV 639 
                                            *********************************************************************** PP

                             TIGR01369  634 ivqlgGqtalnlakeleeagvkilGtsaesidraEdRekFsklldelgikqpkgkeatsveeakeiakeig 704 
                                            ivq+gGqt+ln+ak+le++g+kilGts++sid+aEdRe+F++l+++lgi+qp++ +a+s+eeakeia++ig
  NCBI__GCF_000194625.1:WP_013684200.1  640 IVQFGGQTPLNIAKQLESSGAKILGTSVDSIDIAEDRERFAELCNRLGIPQPENGIAHSIEEAKEIAARIG 710 
                                            *********************************************************************** PP

                             TIGR01369  705 yPvlvRpsyvlgGrameiveneeeleryleeavevskekPvlidkyledavEvdvDavadgeevliagile 775 
                                            yPvlvRpsyvlgGrameiv++ee+lery++ea+evs+ekP+lidk+leda+Ev+vDa++dgeev+i gi+e
  NCBI__GCF_000194625.1:WP_013684200.1  711 YPVLVRPSYVLGGRAMEIVYDEETLERYISEALEVSPEKPILIDKFLEDAIEVEVDALCDGEEVVIGGIME 781 
                                            *********************************************************************** PP

                             TIGR01369  776 HiEeaGvHsGDstlvlppqklseevkkkikeivkkiakelkvkGllniqfvvkdeevyviEvnvRasRtvP 846 
                                            HiEeaGvHsGDs++vlpp +ls+++ ++i ++++k+a el+v+Gl+niq++vkd+ vyv+E+n+RasRtvP
  NCBI__GCF_000194625.1:WP_013684200.1  782 HIEEAGVHSGDSACVLPPVSLSQDIIDRIVDYTRKMALELNVVGLINIQYAVKDNIVYVLEANPRASRTVP 852 
                                            *********************************************************************** PP

                             TIGR01369  847 fvskalgvplvklavkvllgkkleelekgvkkekksklvavkaavfsfsklagvdvvlgpemkstGEvmgi 917 
                                            fvska+g+pl+k+a+k+++gkkl+e   gvk++ + k+vavk+avf+f kl gvd+vlgpemkstGEvmgi
  NCBI__GCF_000194625.1:WP_013684200.1  853 FVSKATGIPLAKIAAKLMTGKKLKE--LGVKERLNLKHVAVKEAVFPFIKLPGVDPVLGPEMKSTGEVMGI 921 
                                            *************************..679***************************************** PP

                             TIGR01369  918 grdleeallkallaskakikkkgsvllsvkdkdkeellelakklaekglkvyategtakvleeagikaevv 988 
                                            ++d+  a++ka la++++++++g+v++svk++d+e++l++akklae+g+k++at+gta++l+ +gi+ae v
  NCBI__GCF_000194625.1:WP_013684200.1  922 DYDFGVAYYKAELAAGMRLPTEGTVFISVKKEDRERVLPVAKKLAELGFKIIATNGTANFLRANGIDAEIV 992 
                                            *********************************************************************** PP

                             TIGR01369  989 lkvseeaekilellkeeeielvinltskkkkaaekgykirreaveykvplvteletaealle 1050
                                            +kvs+ +++il+++ +++++l+in++s +k+ +++gy+irr+av++++p++t++++a a+++
  NCBI__GCF_000194625.1:WP_013684200.1  993 NKVSQGRPNILDVIINRQVDLIINTPS-GKRGKTEGYMIRRAAVDHNIPYITTVSGAIAAVK 1053
                                            ************************998.888999*******************999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1052 nodes)
Target sequences:                          1  (1076 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 34.15
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis