Alignments for a candidate for carB in Bacteroides thetaiotaomicron VPI-5482

GapMind for Amino acid biosynthesis

Alignments for a candidate for carB in Bacteroides thetaiotaomicron VPI-5482

Align Carbamoyl-phosphate synthase arginine-specific large chain; Arginine-specific carbamoyl-phosphate synthetase, ammonia chain; EC 6.3.5.5 (characterized)
to candidate 353392 BT3866 glutamine-dependent carbamyl phosphate synthetase (NCBI ptt file)

Query= SwissProt::P03965
         (1118 letters)



>FitnessBrowser__Btheta:353392
          Length = 1073

 Score = 1013 bits (2620), Expect = 0.0
 Identities = 548/1092 (50%), Positives = 731/1092 (66%), Gaps = 31/1092 (2%)

Query: 28   VNSVLVIGSGGLSIGQAGEFDYSGSQAIKALKEDNKFTILVNPNIATNQTSHSLADKIYY 87
            +  VLV+GSG L IGQAGEFDYSGSQA+KALKE+   ++LVNPNIAT QTS  +ADK+Y+
Sbjct: 5    IKKVLVLGSGALKIGQAGEFDYSGSQALKALKEEGISSVLVNPNIATIQTSEGIADKVYF 64

Query: 88   LPVTPEYITYIIELERPDAILLTFGGQTGLNCGVALDESGVLAKYNVKVLGTPIKTLITS 147
            LPVT  ++  II+ ERPD ILL FGGQT LNCG  L   G+L KY VKVLGT ++ ++ +
Sbjct: 65   LPVTTYFVEEIIKKERPDGILLAFGGQTALNCGAELYTQGILDKYGVKVLGTSVEAIMYT 124

Query: 148  EDRDLFASALKDINIPIAESFACETVDEALEAAERVKYPVIVRSAYALGGLGSGFANNAS 207
            EDRDLF   L +IN+    S A E++++A+ AA ++ YPV+VRSAYALGGLGSG   N  
Sbjct: 125  EDRDLFVKKLDEINMKTPVSQAVESMEDAIAAARKIGYPVMVRSAYALGGLGSGICANEE 184

Query: 208  EMKELAAQSLSLAPQILVEKSLKGWKEVEYEVVRDRVGNCITVCNMENFDPLGVHTGDSM 267
            E  +LA  S + + QILVE+SLKGWKE+E+EV+RD   +C TV +MENFDPLG+HTG+S+
Sbjct: 185  EFLKLAESSFAFSKQILVEESLKGWKEIEFEVIRDANDHCFTVASMENFDPLGIHTGESI 244

Query: 268  VFAPSQTLSDEEFHMLRSAAIKIIRHLGVIGECNVQYALQPDGLDYRVIEVNARLSRSSA 327
            V AP+ +L D+E  +L+  + K IRHLG++GECN+QYA   D  DYRVIEVNARLSRSSA
Sbjct: 245  VVAPTCSLDDKELKLLQELSAKCIRHLGIVGECNIQYAFNSDTDDYRVIEVNARLSRSSA 304

Query: 328  LASKATGYPLAYTAAKIGLGYTLPELPNPITKTTVANFEPSLDYIVAKIPKWDLSKFQYV 387
            LASKATGYPLA+ AAKI LGY+L ++    T  + A   P LDY + KIP+WDL+KF  V
Sbjct: 305  LASKATGYPLAFVAAKIALGYSLDQIGEMGTPNS-AYLAPQLDYYICKIPRWDLTKFAGV 363

Query: 388  DRSIGSSMKSVGEVMAIGRNYEEAFQKALRQVDPSLLGFQGSTEFG-DQLDEALRTPTDR 446
             R IGSSMKSVGE+M+IGR++EE  QK LR +   + GF G+ +   D LD+ L  PTD 
Sbjct: 364  SREIGSSMKSVGEIMSIGRSFEEIIQKGLRMIGQGMHGFVGNDDVHFDDLDKELSRPTDL 423

Query: 447  RVLAIGQALIHENYTVERVNELSKIDKWFLYKCMNIVNIYKELESVKSLSDLSKDLLQRA 506
            R+ +I QA+  E Y+++R++EL+KID WFL K  NIV+   +L +   + D+  D+++ A
Sbjct: 424  RIFSIAQAM-EEGYSIDRIHELTKIDPWFLGKLKNIVDYKAKLSTYNKVEDIPADVMREA 482

Query: 507  KKLGFSDKQIA-VTINKHASTNINELEIRSLRKTLGIIPFVKRIDTLAAEFPAQTNYLYT 565
            K LGFSD QIA   +N   +     L +R+ RK LGI+P VKRI+T+A+E P  TNYLY 
Sbjct: 483  KILGFSDFQIARFVLNPTGNMEKENLAVRAHRKALGILPAVKRINTVASEHPELTNYLYM 542

Query: 566  TYNATKNDVEF--NENGMLVLGSGVYRIGSSVEFDWCAVNTAKTLRDQGKKTIMINYNPE 623
            TY     DV +  NE  ++VLGSG YRIGSSVEFDWC+VN  +T R  G K+IMINYNPE
Sbjct: 543  TYAVEGYDVNYYKNEKSVVVLGSGAYRIGSSVEFDWCSVNAVQTARKLGYKSIMINYNPE 602

Query: 624  TVSTDFDEVDRLYFEELSYERVMDIYELEQSEGCIISVGGQLPQNIALKLYDNGCNIMGT 683
            TVSTD+D  DRLYF+ELS+ERV+D+ +LEQ  G I+SVGGQ+P N+A+KLY     ++GT
Sbjct: 603  TVSTDYDMCDRLYFDELSFERVLDVIDLEQPRGVIVSVGGQIPNNLAMKLYRQSVPVLGT 662

Query: 684  NPNDIDRAENRHKFSSILDSIDVDQPEWSELTSVEEAKLFASKVNYPVLIRPSYVLSGAA 743
            +P  IDRAENR+KFS++LD + +DQP W ELTS+EE K F  KV YPVL+RPSYVLSGAA
Sbjct: 663  SPVSIDRAENRNKFSAMLDQLGIDQPAWMELTSLEEVKGFVEKVGYPVLVRPSYVLSGAA 722

Query: 744  MSVVNNEEELKAKLTLASDVSPDHPVVMSKFIEGAQEIDVDAVAYNGNVLVHAISEHVEN 803
            M+V  ++EEL+  L +A++VS ++PVV+S+F+E  +EI+ DAVA NG V+ +AISEHVE 
Sbjct: 723  MNVCYDDEELENFLKMAAEVSKEYPVVVSQFLENTKEIEFDAVAQNGEVVEYAISEHVEF 782

Query: 804  AGVHSGDASLVLPPQHLSDDVKIALKDIADKVAKAWKITGPFNMQIIKDGEHTLKVIECN 863
            AGVHSGDA+LV P Q +       +K I+ ++AK   I+GPFN+Q +    + +KVIECN
Sbjct: 783  AGVHSGDATLVFPAQKIYFATARRIKKISRQIAKELNISGPFNIQFLA-RNNEVKVIECN 841

Query: 864  IRASRSFPFVSKVLGVNFIEIAVKAFLGGDIVPKPVDLMLNKKYDYVATKVPQFSFTRLA 923
            +RASRSFPFVSKVL  NFIE A +  L     P           D++  K  QFSF+RL 
Sbjct: 842  LRASRSFPFVSKVLKRNFIETATRIMLD---APYSQPDKTAFDIDWIGVKASQFSFSRLH 898

Query: 924  GADPFLGVEMASTGEVASFGRDLIESYWTAIQSTMNFHVPLPPSGILFGGDTSREYLGQV 983
             ADP LGV+M+STGEV   G D  E+   A+ +T  F +P        G   S+  L   
Sbjct: 899  KADPVLGVDMSSTGEVGCIGDDFSEALLNAMIAT-GFKIPEKAVMFSSGAMKSKVDLLDA 957

Query: 984  ASIVATIGYRIYTTNETTKTYLQEHIKEKNAKVSLIKFPKND---KRKLRELFQEYDIKA 1040
            + ++   GY+IY T   T  +L  H      + + + +P      +  + ++  ++    
Sbjct: 958  SRMLFAKGYQIYAT-AGTAAFLNAH----GVETTPVYWPDEKPGAENNVMKMIADHKFDL 1012

Query: 1041 VFNLASKRAESTDDVDYIMRRNAIDFAIPLFNEPQTALLFAKCLKAKIAEKIKILESHDV 1100
            + N+    ++      Y +RR AID  IPL    + A  F         E    L+  D+
Sbjct: 1013 IVNIPKNHSKRELTNGYRIRRGAIDHNIPLITNARLASAF--------IEAFCELKLSDI 1064

Query: 1101 IVPPEVRSWDEF 1112
                +++SW E+
Sbjct: 1065 ----QIKSWQEY 1072



 Score =  155 bits (392), Expect = 2e-41
 Identities = 107/406 (26%), Positives = 198/406 (48%), Gaps = 24/406 (5%)

Query: 15  FTTEDYKPQLVEGVNSVLVIGSGGLSIGQAGEFDYSGSQAIKALKEDNKFTILVNPNIAT 74
           +  E Y     +   SV+V+GSG   IG + EFD+    A++  ++    +I++N N  T
Sbjct: 544 YAVEGYDVNYYKNEKSVVVLGSGAYRIGSSVEFDWCSVNAVQTARKLGYKSIMINYNPET 603

Query: 75  NQTSHSLADKIYYLPVTPEYITYIIELERPDAILLTFGGQTGLNCGVALDESGVLAKYNV 134
             T + + D++Y+  ++ E +  +I+LE+P  ++++ GGQ   N  +       L + +V
Sbjct: 604 VSTDYDMCDRLYFDELSFERVLDVIDLEQPRGVIVSVGGQIPNNLAMK------LYRQSV 657

Query: 135 KVLGTPIKTLITSEDRDLFASALKDINIPIAESFACETVDEALEAAERVKYPVIVRSAYA 194
            VLGT   ++  +E+R+ F++ L  + I         +++E     E+V YPV+VR +Y 
Sbjct: 658 PVLGTSPVSIDRAENRNKFSAMLDQLGIDQPAWMELTSLEEVKGFVEKVGYPVLVRPSYV 717

Query: 195 LGGLGSGFANNASEMKELAAQSLSLAPQ--ILVEKSLKGWKEVEYEVVRDRVGNCITVCN 252
           L G       +  E++     +  ++ +  ++V + L+  KE+E++ V    G  +    
Sbjct: 718 LSGAAMNVCYDDEELENFLKMAAEVSKEYPVVVSQFLENTKEIEFDAVAQN-GEVVEYAI 776

Query: 253 MENFDPLGVHTGDSMVFAPSQTLSDEEFHMLRSAAIKIIRHLGVIGECNVQYALQPDGLD 312
            E+ +  GVH+GD+ +  P+Q +       ++  + +I + L + G  N+Q+  + +  +
Sbjct: 777 SEHVEFAGVHSGDATLVFPAQKIYFATARRIKKISRQIAKELNISGPFNIQFLARNN--E 834

Query: 313 YRVIEVNARLSRSSALASKATGYPLAYTAAKIGLG--YTLPELPNPITKTTVANFEPSLD 370
            +VIE N R SRS    SK        TA +I L   Y+ P+      KT        +D
Sbjct: 835 VKVIECNLRASRSFPFVSKVLKRNFIETATRIMLDAPYSQPD------KTAF-----DID 883

Query: 371 YIVAKIPKWDLSKFQYVDRSIGSSMKSVGEVMAIGRNYEEAFQKAL 416
           +I  K  ++  S+    D  +G  M S GEV  IG ++ EA   A+
Sbjct: 884 WIGVKASQFSFSRLHKADPVLGVDMSSTGEVGCIGDDFSEALLNAM 929


Lambda     K      H
   0.317    0.134    0.380 

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: 2683
Number of extensions: 106
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: 1118
Length of database: 1073
Length adjustment: 46
Effective length of query: 1072
Effective length of database: 1027
Effective search space:  1100944
Effective search space used:  1100944
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 (21.6 bits)
S2: 58 (26.9 bits)

Align candidate 353392 BT3866 (glutamine-dependent carbamyl phosphate synthetase (NCBI ptt file))
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.15017.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 1452.1   0.1          0 1451.9   0.1    1.0  1  lcl|FitnessBrowser__Btheta:353392  BT3866 glutamine-dependent carba


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:353392  BT3866 glutamine-dependent carbamyl phosphate synthetase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1451.9   0.1         0         0       3    1051 ..       2    1055 ..       1    1056 [. 0.98

  Alignments for each domain:
  == domain 1  score: 1451.9 bits;  conditional E-value: 0
                          TIGR01369    3 redikkvlviGsGpivigqAaEFDYsGsqalkalkeegievvLvnsniAtvmtdeeladkvYiePltveaveki 76  
                                         +++ikkvlv+GsG+++igqA+EFDYsGsqalkalkeegi+ vLvn+niAt++t+e +adkvY++P+t+++ve+i
  lcl|FitnessBrowser__Btheta:353392    2 EKEIKKVLVLGSGALKIGQAGEFDYSGSQALKALKEEGISSVLVNPNIATIQTSEGIADKVYFLPVTTYFVEEI 75  
                                         579*********************************************************************** PP

                          TIGR01369   77 iekErpDailltlGGqtaLnlaveleekGvLekygvkllGtkveaikkaedRekFkealkeineevakseives 150 
                                         i+kErpD+ill++GGqtaLn++ el  +G+L+kygvk+lGt+veai+ +edR++F ++l+ein++++ s++ves
  lcl|FitnessBrowser__Btheta:353392   76 IKKERPDGILLAFGGQTALNCGAELYTQGILDKYGVKVLGTSVEAIMYTEDRDLFVKKLDEINMKTPVSQAVES 149 
                                         ************************************************************************** PP

                          TIGR01369  151 veealeaaeeigyPvivRaaftlgGtGsgiaeneeelkelvekalkaspikqvlvekslagwkEiEyEvvRDsk 224 
                                         +e+a++aa++igyPv+vR+a++lgG Gsgi+ neee+ +l+e++++ s  kq+lve+sl+gwkEiE+Ev+RD++
  lcl|FitnessBrowser__Btheta:353392  150 MEDAIAAARKIGYPVMVRSAYALGGLGSGICANEEEFLKLAESSFAFS--KQILVEESLKGWKEIEFEVIRDAN 221 
                                         ************************************************..************************ PP

                          TIGR01369  225 dnciivcniEnlDplGvHtGdsivvaPsqtLtdkeyqllRdaslkiirelgvegecnvqfaldPeskryvviEv 298 
                                         d+c +v+++En+DplG+HtG+sivvaP+  L+dke +ll + s k ir+lg++gecn+q+a + ++ +y+viEv
  lcl|FitnessBrowser__Btheta:353392  222 DHCFTVASMENFDPLGIHTGESIVVAPTCSLDDKELKLLQELSAKCIRHLGIVGECNIQYAFNSDTDDYRVIEV 295 
                                         ************************************************************************** PP

                          TIGR01369  299 npRvsRssALAskAtGyPiAkvaaklavGysLdelkndvtketvAsfEPslDYvvvkiPrwdldkfekvdrklg 372 
                                         n+R+sRssALAskAtGyP+A vaak+a+GysLd++    t + +A   P lDY ++kiPrwdl kf++v+r++g
  lcl|FitnessBrowser__Btheta:353392  296 NARLSRSSALASKATGYPLAFVAAKIALGYSLDQIGEMGTPN-SAYLAPQLDYYICKIPRWDLTKFAGVSREIG 368 
                                         ***********************************9888875.5****************************** PP

                          TIGR01369  373 tqmksvGEvmaigrtfeealqkalrsleekllglklkekeaesdeeleealkkpndrRlfaiaealrrgvsvee 446 
                                         ++mksvGE+m+igr+fee +qk+lr++ ++++g+  +++++ +d +  ++l +p+d R+f ia+a+ +g+s+++
  lcl|FitnessBrowser__Btheta:353392  369 SSMKSVGEIMSIGRSFEEIIQKGLRMIGQGMHGFVGNDDVHFDDLD--KELSRPTDLRIFSIAQAMEEGYSIDR 440 
                                         ************************************9887777766..99************************ PP

                          TIGR01369  447 vyeltkidrffleklkklvelekeleee.klkelkkellkkakklGfsdeqiaklvk.......vseaevrklr 512 
                                         ++eltkid +fl klk++v+ + +l++  k+++++++++++ak lGfsd qia++v        +++ +vr+ r
  lcl|FitnessBrowser__Btheta:353392  441 IHELTKIDPWFLGKLKNIVDYKAKLSTYnKVEDIPADVMREAKILGFSDFQIARFVLnptgnmeKENLAVRAHR 514 
                                         *************************9877899**********************998555554455555***** PP

                          TIGR01369  513 kelgivpvvkrvDtvaaEfeaktpYlYstyeeekddvevtek.kkvlvlGsGpiRigqgvEFDycavhavlalr 585 
                                         k+lgi+p+vkr++tva+E++  t+YlY ty+ e  dv++ ++ k+v+vlGsG++Rig++vEFD+c+v+av++ r
  lcl|FitnessBrowser__Btheta:353392  515 KALGILPAVKRINTVASEHPELTNYLYMTYAVEGYDVNYYKNeKSVVVLGSGAYRIGSSVEFDWCSVNAVQTAR 588 
                                         *********************************888876555499***************************** PP

                          TIGR01369  586 eagyktilinynPEtvstDydiadrLyFeeltvedvldiiekekvegvivqlgGqtalnlakeleeagvkilGt 659 
                                         + gyk+i+inynPEtvstDyd++drLyF+el++e+vld+i+ e+++gviv++gGq+++nla++l+++ v++lGt
  lcl|FitnessBrowser__Btheta:353392  589 KLGYKSIMINYNPETVSTDYDMCDRLYFDELSFERVLDVIDLEQPRGVIVSVGGQIPNNLAMKLYRQSVPVLGT 662 
                                         ************************************************************************** PP

                          TIGR01369  660 saesidraEdRekFsklldelgikqpkgkeatsveeakeiakeigyPvlvRpsyvlgGrameiveneeeleryl 733 
                                         s+ sidraE+R+kFs++ld+lgi+qp+++e+ts+ee+k +++++gyPvlvRpsyvl+G+am++++++eele++l
  lcl|FitnessBrowser__Btheta:353392  663 SPVSIDRAENRNKFSAMLDQLGIDQPAWMELTSLEEVKGFVEKVGYPVLVRPSYVLSGAAMNVCYDDEELENFL 736 
                                         ************************************************************************** PP

                          TIGR01369  734 eeavevskekPvlidkyledavEvdvDavadgeevliagileHiEeaGvHsGDstlvlppqklseevkkkikei 807 
                                         + a+evske+Pv+++++le+++E++ Dava+++ev+ ++i+eH+E aGvHsGD+tlv+p+qk+   + ++ik+i
  lcl|FitnessBrowser__Btheta:353392  737 KMAAEVSKEYPVVVSQFLENTKEIEFDAVAQNGEVVEYAISEHVEFAGVHSGDATLVFPAQKIYFATARRIKKI 810 
                                         ************************************************************************** PP

                          TIGR01369  808 vkkiakelkvkGllniqfvvkdeevyviEvnvRasRtvPfvskalgvplvklavkvllgkkleelekgvkkekk 881 
                                         +++iakel+++G++niqf+++++ev+viE+n+RasR++Pfvsk+l+ +++++a++++l++  ++ +k   +  +
  lcl|FitnessBrowser__Btheta:353392  811 SRQIAKELNISGPFNIQFLARNNEVKVIECNLRASRSFPFVSKVLKRNFIETATRIMLDAPYSQPDK---TAFD 881 
                                         **************************************************************99776...8999 PP

                          TIGR01369  882 sklvavkaavfsfsklagvdvvlgpemkstGEvmgigrdleeallkallaskakikkkgsvllsvkdkdkeell 955 
                                          + ++vka++fsfs+l+++d+vlg++m stGEv +ig+d++eall a++a+++ki++k+++++s++ k+k +ll
  lcl|FitnessBrowser__Btheta:353392  882 IDWIGVKASQFSFSRLHKADPVLGVDMSSTGEVGCIGDDFSEALLNAMIATGFKIPEKAVMFSSGAMKSKVDLL 955 
                                         9************************************************************************* PP

                          TIGR01369  956 elakklaekglkvyategtakvleeagikaevvlkvseea...ekilellkeeeielvinltskkkk.aaekgy 1025
                                         ++ ++l +kg+++yat+gta++l+ +g++++ v++  e+    +++++++++++++l++n++++++k + ++gy
  lcl|FitnessBrowser__Btheta:353392  956 DASRMLFAKGYQIYATAGTAAFLNAHGVETTPVYWPDEKPgaeNNVMKMIADHKFDLIVNIPKNHSKrELTNGY 1029
                                         ************************************999888899****************9876654899*** PP

                          TIGR01369 1026 kirreaveykvplvteletaeallea 1051
                                         +irr a+++++pl+t++++a+a++ea
  lcl|FitnessBrowser__Btheta:353392 1030 RIRRGAIDHNIPLITNARLASAFIEA 1055
                                         ***********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (1052 nodes)
Target sequences:                          1  (1073 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: 0.09u 0.03s 00:00:00.12 Elapsed: 00:00:00.12
# Mc/sec: 8.90
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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