Alignments for a candidate for acs in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Phaeobacter inhibens BS107

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate GFF1279 PGA1_c12950 acetyl-coenzyme A synthetase Acs

Query= reanno::pseudo3_N2E3:AO353_03060
         (651 letters)



>FitnessBrowser__Phaeo:GFF1279
          Length = 695

 Score =  833 bits (2153), Expect = 0.0
 Identities = 411/644 (63%), Positives = 477/644 (74%), Gaps = 5/644 (0%)

Query: 2   SAASLYPVRPEVAANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFD 61
           S +  Y    E  A    + A Y  MY  S+ +P+GFWR+QA+R+DWIKPFT VK   F 
Sbjct: 47  SDSKAYAPSEETVARAHVNAAQYDEMYAASMQDPEGFWRQQAERIDWIKPFTQVKDVDFT 106

Query: 62  DHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPAES-RNITYRELHEQVCKF 120
             +V I W+ADGTLNV+ NC+DRHL  RGDQ AIIWE D P E+ ++I+Y++LH +VC+ 
Sbjct: 107 LGNVSINWYADGTLNVAANCIDRHLDTRGDQTAIIWEPDSPDEAAQHISYKQLHTRVCRM 166

Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180
           AN L    V +GD V IY+PMIPEA  AMLAC RIGAIHS+VF GFSP+ALA R+  C +
Sbjct: 167 ANVLETMGVRKGDRVVIYLPMIPEAAYAMLACARIGAIHSIVFAGFSPDALAARVNGCDA 226

Query: 181 KVVITADEGLRAGKKISLKANVDDALTNPETSSIQKVIVCKRTGGNIKWNQHRDIWYEDL 240
           KV+ITADE  R G+K  LK+N D AL +  T    K +V KRTGG   W   RD  Y ++
Sbjct: 227 KVLITADEAPRGGRKTPLKSNADAALLH--TKDTVKCLVVKRTGGQTTWIDGRDYDYNEM 284

Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAALTHERVFDYRPGEI 300
              A     P EM AE+ LFILYTSGSTG+PKGV HTTGGYL YAA+THE  FDY  G+I
Sbjct: 285 ALEADDYSKPAEMNAEDPLFILYTSGSTGQPKGVVHTTGGYLTYAAMTHEITFDYHDGDI 344

Query: 301 YWCTADVGWVTGHTYIVYGPLANGATTLLFEGVPNYPDITRVAKIIDKHKVNILYTAPTA 360
           YWCTADVGWVTGH+YIVYGPLANGATTL+FEGVP YPD +R  ++ DKHKV   YTAPTA
Sbjct: 345 YWCTADVGWVTGHSYIVYGPLANGATTLMFEGVPTYPDASRFWQVCDKHKVTQFYTAPTA 404

Query: 361 IRAMMAQGTAAVEGADGSSLRLLGSVGEPINPEAWEWYYKNVGQSRCPIVDTWWQTETGA 420
           +RA+M QG   VE  D SSLR LG+VGEPINPEAW WY   VG+ +CPIVDTWWQTETG 
Sbjct: 405 LRALMGQGNEWVEKCDLSSLRTLGTVGEPINPEAWNWYNDIVGKGKCPIVDTWWQTETGG 464

Query: 421 TLMSPLPGAHGLKPGSAARPFFGVVPALVD-NLGNIIEG-VAEGNLVILDSWPGQARTLY 478
            LM+PLPGAH  KPG+A +PFFGV P ++D   G  I G   EG L I DSWPGQ RT++
Sbjct: 465 HLMTPLPGAHATKPGAAMKPFFGVAPVVLDPQSGEEITGNGVEGVLCIKDSWPGQMRTVW 524

Query: 479 GDHDRFVDTYFKTFRGMYFTGDGARRDADGYWWITGRVDDVLNVSGHRMGTAEIESAMVA 538
           GDH+RF  TYF  ++G YFTGDG RRD DG +WITGRVDDV+NVSGHRMGTAE+ESA+VA
Sbjct: 525 GDHERFEKTYFSDYKGYYFTGDGCRRDEDGDYWITGRVDDVINVSGHRMGTAEVESALVA 584

Query: 539 HPKVAEAAVVGVPHDIKGQGIYVYVTLNGGEEPSEALRLELKNWVRKEIGPIASPDVIQW 598
           H  VAEAAVVG PH+IKGQGIY YVTL    EPS+ L  EL+ WVR EIGPIASPDVIQW
Sbjct: 585 HAAVAEAAVVGYPHEIKGQGIYCYVTLMNDREPSDELVKELRTWVRTEIGPIASPDVIQW 644

Query: 599 APGLPKTRSGKIMRRILRKIATGEYDGLGDISTLADPGVVQHLI 642
           APGLPKTRSGKIMRRILRKIA  ++  LGD STLADP VV  LI
Sbjct: 645 APGLPKTRSGKIMRRILRKIAENDFGSLGDTSTLADPSVVDDLI 688


Lambda     K      H
   0.319    0.136    0.425 

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: 1580
Number of extensions: 86
Number of successful extensions: 4
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: 695
Length adjustment: 39
Effective length of query: 612
Effective length of database: 656
Effective search space:   401472
Effective search space used:   401472
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate GFF1279 PGA1_c12950 (acetyl-coenzyme A synthetase Acs)
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.27319.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 1013.5   0.2          0 1013.2   0.2    1.0  1  lcl|FitnessBrowser__Phaeo:GFF1279  PGA1_c12950 acetyl-coenzyme A sy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF1279  PGA1_c12950 acetyl-coenzyme A synthetase Acs
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1013.2   0.2         0         0       3     628 ..      65     689 ..      63     690 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1013.2 bits;  conditional E-value: 0
                          TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdkva 75 
                                        ++ +y e+y+ +++dpe fw+++a+ +++w+kpf++v+d +++    +++W++dg+lnv++nc+drh+ +r d++a
  lcl|FitnessBrowser__Phaeo:GFF1279  65 NAAQYDEMYAASMQDPEGFWRQQAE-RIDWIKPFTQVKDVDFTLgnvSINWYADGTLNVAANCIDRHLDTRGDQTA 139
                                        6789********************9.5**************9877789**************************** PP

                          TIGR02188  76 iiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsae 151
                                        iiwe d+++e +++++Y++l+++vcr+anvl+++Gv+kgdrv+iYlpmipea++amlacaRiGa+hs+vfaGfs++
  lcl|FitnessBrowser__Phaeo:GFF1279 140 IIWEPDSPDEAAQHISYKQLHTRVCRMANVLETMGVRKGDRVVIYLPMIPEAAYAMLACARIGAIHSIVFAGFSPD 215
                                        **************************************************************************** PP

                          TIGR02188 152 alaeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwweelvekea 227
                                        ala R++ ++ak++itade+ Rgg++++lk+++d+al +++++v+ +lvvkrtg + ++w +grD+ ++e+  + a
  lcl|FitnessBrowser__Phaeo:GFF1279 216 ALAARVNGCDAKVLITADEAPRGGRKTPLKSNADAALLHTKDTVK-CLVVKRTGGQ-TTWIDGRDYDYNEMALE-A 288
                                        ****************************************98776.**********.56***********9995.* PP

                          TIGR02188 228 saecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygP 303
                                        +++ +p+++++edplfiLYtsGstG+PkGv+httgGyl++aa+t++++fd++d+di+wCtaDvGWvtGhsYivygP
  lcl|FitnessBrowser__Phaeo:GFF1279 289 DDYSKPAEMNAEDPLFILYTSGSTGQPKGVVHTTGGYLTYAAMTHEITFDYHDGDIYWCTADVGWVTGHSYIVYGP 364
                                        **************************************************************************** PP

                          TIGR02188 304 LanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeawe 379
                                        LanGattl+fegvptypdasrfw+v++k+kvt+fYtaPta+Ralm +g+e+v+k dlsslr lg+vGepinpeaw+
  lcl|FitnessBrowser__Phaeo:GFF1279 365 LANGATTLMFEGVPTYPDASRFWQVCDKHKVTQFYTAPTALRALMGQGNEWVEKCDLSSLRTLGTVGEPINPEAWN 440
                                        **************************************************************************** PP

                          TIGR02188 380 WyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvd.eegkeveeeeeggvLvikkp 454
                                        Wy++ vGk+kcpivdtwWqtetGg+l+tplpg a ++kpg+a++P+fG+ ++v+d ++g+e++ +  +gvL+ik++
  lcl|FitnessBrowser__Phaeo:GFF1279 441 WYNDIVGKGKCPIVDTWWQTETGGHLMTPLPG-AHATKPGAAMKPFFGVAPVVLDpQSGEEITGNGVEGVLCIKDS 515
                                        ********************************.6*********************999*****555559******* PP

                          TIGR02188 455 wPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaea 530
                                        wP+++rt++gd+erf +tYf+++kg+yftGDg+rrd+dG++wi+GRvDdvinvsGhr+gtae+esalv+h avaea
  lcl|FitnessBrowser__Phaeo:GFF1279 516 WPGQMRTVWGDHERFEKTYFSDYKGYYFTGDGCRRDEDGDYWITGRVDDVINVSGHRMGTAEVESALVAHAAVAEA 591
                                        **************************************************************************** PP

                          TIGR02188 531 avvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiae 606
                                        avvg+p+eikg+ i+++v+l++ +e+++e l kel+++vr+eigpia+pd i++++ lPktRsGkimRR+lrkiae
  lcl|FitnessBrowser__Phaeo:GFF1279 592 AVVGYPHEIKGQGIYCYVTLMNDREPSDE-LVKELRTWVRTEIGPIASPDVIQWAPGLPKTRSGKIMRRILRKIAE 666
                                        ****************************5.********************************************** PP

                          TIGR02188 607 ge.ellgdvstledpsvveelke 628
                                        ++  +lgd+stl+dpsvv++l++
  lcl|FitnessBrowser__Phaeo:GFF1279 667 NDfGSLGDTSTLADPSVVDDLIA 689
                                        *******************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (695 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 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 13.31
//
[ok]

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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

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 catabolism of small carbon sources