GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acs in Dyella japonica UNC79MFTsu3.2

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate N515DRAFT_3075 N515DRAFT_3075 acetyl-coenzyme A synthetase (EC 6.2.1.1)

Query= reanno::pseudo5_N2C3_1:AO356_18695
         (651 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_3075 N515DRAFT_3075
           acetyl-coenzyme A synthetase (EC 6.2.1.1)
          Length = 646

 Score =  909 bits (2350), Expect = 0.0
 Identities = 432/640 (67%), Positives = 514/640 (80%)

Query: 4   ASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDH 63
           + +YPV+PE AA     +  Y+ +Y++SV +P+GFW    +RL+W +  + +K  S+D  
Sbjct: 2   SKVYPVKPEFAAKARISKEDYERLYEESVRDPEGFWGRIGERLEWHRKPSKIKNVSYDPK 61

Query: 64  HVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANA 123
           ++ I+W+ DG LNVS NCLDRHLA RGD+ AII+EGDDP+ESR++TYRELH EVCKFAN 
Sbjct: 62  NLHIRWYEDGELNVSANCLDRHLASRGDKTAIIFEGDDPNESRHLTYRELHAEVCKFANT 121

Query: 124 LRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVV 183
           L+   V +GD V IYMPMIPEA VAMLAC RIGA+HSVVFGGFSP++LAGRI D  +KVV
Sbjct: 122 LKNLGVAKGDRVAIYMPMIPEAAVAMLACARIGAVHSVVFGGFSPDSLAGRIADSTAKVV 181

Query: 184 ITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKV 243
           +TADEGVR GKKIPLKANVD AL  P T+S++ VIV +RT   +     RD +Y  LM+ 
Sbjct: 182 VTADEGVRGGKKIPLKANVDAALERPGTNSVETVIVVRRTGSAVPMQSPRDRYYHVLMEG 241

Query: 244 AGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWC 303
               C P  + AE  LFILYTSGSTGKPKGV HT+ GYL++A  THE VFD +  +VYWC
Sbjct: 242 QSADCPPTPVEAEHPLFILYTSGSTGKPKGVLHTSGGYLVFAGFTHEMVFDLREDDVYWC 301

Query: 304 TADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRA 363
           TADVGWVTGHSY+VYGPLANGATT++F+GVPNYPD +R   V+DKHKV++ YTAPTAIRA
Sbjct: 302 TADVGWVTGHSYVVYGPLANGATTVMFDGVPNYPDTSRFWNVVDKHKVTLFYTAPTAIRA 361

Query: 364 MMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLI 423
           +M  G A V+ A  +SLRLLGSVGEPINPEAW+WYY+ VG ERCPIVDTWWQTETGG++I
Sbjct: 362 LMREGEAPVKKASRASLRLLGSVGEPINPEAWEWYYRVVGDERCPIVDTWWQTETGGIMI 421

Query: 424 SPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDR 483
           +PL GA   KPGSAT+PFFG+ PA+VD  G ++EGA EGNLVI DSWPGQ RT+YGDH R
Sbjct: 422 TPLAGAIDAKPGSATKPFFGIRPAVVDAGGAVLEGATEGNLVIADSWPGQMRTVYGDHQR 481

Query: 484 FVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVA 543
           FV+TYF  + G YFTGDG RRDEDGYYWITGRVDDV+NVSGHR+GTAE+ESA+V+HPKVA
Sbjct: 482 FVETYFTAYPGNYFTGDGVRRDEDGYYWITGRVDDVINVSGHRIGTAEVESALVSHPKVA 541

Query: 544 EAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLP 603
           EAAVVG PH+IKGQGIY YVTL AGE+ S+ LR EL  WVRKEIGPIA+PD +QWAPGLP
Sbjct: 542 EAAVVGCPHEIKGQGIYAYVTLIAGEQGSDELRKELVAWVRKEIGPIATPDYLQWAPGLP 601

Query: 604 KTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIE 643
           KTRSGKIMRRILRKI   + D LGDISTLADP VV +L+E
Sbjct: 602 KTRSGKIMRRILRKIGENQPDQLGDISTLADPSVVKNLVE 641


Lambda     K      H
   0.318    0.135    0.418 

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: 1422
Number of extensions: 75
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 651
Length of database: 646
Length adjustment: 38
Effective length of query: 613
Effective length of database: 608
Effective search space:   372704
Effective search space used:   372704
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: 54 (25.4 bits)

Align candidate N515DRAFT_3075 N515DRAFT_3075 (acetyl-coenzyme A synthetase (EC 6.2.1.1))
to HMM TIGR02188 (acs: acetate--CoA ligase (EC 6.2.1.1))

# 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.carbon/TIGR02188.hmm
# target sequence database:        /tmp/gapView.27184.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02188  [M=629]
Accession:   TIGR02188
Description: Ac_CoA_lig_AcsA: acetate--CoA ligase
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 1024.9   0.0          0 1024.7   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_3075  N515DRAFT_3075 acetyl-coenzyme A


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_3075  N515DRAFT_3075 acetyl-coenzyme A synthetase (EC 6.2.1.1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1024.7   0.0         0         0       3     628 ..      18     641 ..      16     642 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1024.7 bits;  conditional E-value: 0
                                    TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdr 65 
                                                  + e+y++lyee+++dpe fw++ ++ +lew+++ +k+++ s +p   +++W+edgelnvs+nc+dr
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3075  18 SKEDYERLYEESVRDPEGFWGRIGE-RLEWHRKPSKIKNVSYDPknlHIRWYEDGELNVSANCLDR 82 
                                                  5789********************9.5************9998877899***************** PP

                                    TIGR02188  66 hvekrkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviam 131
                                                  h+++r dk+aii+egd+++e sr+ltY+el++evc++an+lk+lGv kgdrvaiY+pmipea++am
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3075  83 HLASRGDKTAIIFEGDDPNE-SRHLTYRELHAEVCKFANTLKNLGVAKGDRVAIYMPMIPEAAVAM 147
                                                  ******************96.********************************************* PP

                                    TIGR02188 132 lacaRiGavhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.sve 196
                                                  lacaRiGavhsvvf+Gfs+++la Ri d++ak+v+tadeg+Rggk+i+lk++vd+ale+  + sve
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3075 148 LACARIGAVHSVVFGGFSPDSLAGRIADSTAKVVVTADEGVRGGKKIPLKANVDAALERPGTnSVE 213
                                                  ***********************************************************9988*** PP

                                    TIGR02188 197 kvlvvkrtgeevaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttg 262
                                                  +v+vv+rtg+ v  +++ rD +++ l+e ++sa+c+p+++++e+plfiLYtsGstGkPkGvlht+g
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3075 214 TVIVVRRTGSAVP-MQSPRDRYYHVLME-GQSADCPPTPVEAEHPLFILYTSGSTGKPKGVLHTSG 277
                                                  ***********66.**************.6************************************ PP

                                    TIGR02188 263 GylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfwev 328
                                                  Gyl+ a  t+++vfd++++d++wCtaDvGWvtGhsY+vygPLanGatt++f+gvp+ypd+srfw+v
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3075 278 GYLVFAGFTHEMVFDLREDDVYWCTADVGWVTGHSYVVYGPLANGATTVMFDGVPNYPDTSRFWNV 343
                                                  ****************************************************************** PP

                                    TIGR02188 329 iekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivd 394
                                                  ++k+kvt fYtaPtaiRalm++ge+ vkk ++ slr+lgsvGepinpeaweWyy+vvG+e+cpivd
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3075 344 VDKHKVTLFYTAPTAIRALMREGEAPVKKASRASLRLLGSVGEPINPEAWEWYYRVVGDERCPIVD 409
                                                  ****************************************************************** PP

                                    TIGR02188 395 twWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlr 460
                                                  twWqtetGgi+itpl+g a+++kpgsat+P+fGi+++vvd  g  +e  +e g Lvi ++wP+++r
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3075 410 TWWQTETGGIMITPLAG-AIDAKPGSATKPFFGIRPAVVDAGGAVLEGATE-GNLVIADSWPGQMR 473
                                                  *****************.6***************************97777.79************ PP

                                    TIGR02188 461 tiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvshea 526
                                                  t+ygd++rfvetYf++++g yftGDg+rrd+dGy+wi+GRvDdvinvsGhr+gtae+esalvsh++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3075 474 TVYGDHQRFVETYFTAYPGNYFTGDGVRRDEDGYYWITGRVDDVINVSGHRIGTAEVESALVSHPK 539
                                                  ****************************************************************** PP

                                    TIGR02188 527 vaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktR 592
                                                  vaeaavvg p+eikg+ i+a+v+l +g++ ++ el+kel ++vrkeigpia+pd +++++ lPktR
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3075 540 VAEAAVVGCPHEIKGQGIYAYVTLIAGEQGSD-ELRKELVAWVRKEIGPIATPDYLQWAPGLPKTR 604
                                                  *****************************999.5******************************** PP

                                    TIGR02188 593 sGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                                  sGkimRR+lrki e++ ++lgd+stl+dpsvv++l e
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3075 605 SGKIMRRILRKIGENQpDQLGDISTLADPSVVKNLVE 641
                                                  *********************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (646 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: 0.03u 0.02s 00:00:00.05 Elapsed: 00:00:00.05
# Mc/sec: 7.65
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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:

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:

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:

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, or view the source code.

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