Aligments for a candidate for acs in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Aligments for a candidate for acs in Shewanella amazonensis SB2B

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate 6937938 Sama_2079 acetyl-CoA synthetase (RefSeq)

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



>lcl|FitnessBrowser__SB2B:6937938 Sama_2079 acetyl-CoA synthetase
           (RefSeq)
          Length = 650

 Score =  973 bits (2516), Expect = 0.0
 Identities = 453/644 (70%), Positives = 533/644 (82%)

Query: 1   MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60
           MS  SLY V  ++AA+ L +   Y+ MYQ+SV NP+GFW E AKR+DWIKPFT VK TS+
Sbjct: 1   MSTQSLYSVPADIAANALVNNEQYQKMYQESVANPEGFWGEHAKRIDWIKPFTQVKDTSY 60

Query: 61  DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKF 120
           DD ++ IKWF DGTLN S NCLDRHLA +GD +AIIWEGDD SE R +TYRELH EVC+F
Sbjct: 61  DDQNLYIKWFHDGTLNASANCLDRHLASKGDDVAIIWEGDDASEQRKVTYRELHAEVCQF 120

Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180
           ANAL+ + V RGDVVTIYMPM+ EA VAMLAC RIGA+HSVVFGGFSP+++A R+ID KS
Sbjct: 121 ANALKAEGVKRGDVVTIYMPMVVEATVAMLACARIGAVHSVVFGGFSPDSIASRVIDGKS 180

Query: 181 KVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDL 240
           K++ITADEGVR G+KIPLK N+D+AL  P+ ++++ VIV KRT G + W + RD W+  +
Sbjct: 181 KLLITADEGVRGGRKIPLKGNIDEALNRPDVTTVETVIVLKRTGGAVNWVEGRDKWWHQV 240

Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEV 300
              A T CA +EMGAE+ LF+LYTSGSTG PKGV HTT GYL+YA++THE VFDYKPGEV
Sbjct: 241 TDGAATECAVEEMGAEDPLFLLYTSGSTGNPKGVLHTTGGYLVYASMTHEYVFDYKPGEV 300

Query: 301 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTA 360
           YWCTADVGW+TGHSY+VYGPLANGAT L+ EG+PN+P   R+ +++D+H+V+ILYTAPT 
Sbjct: 301 YWCTADVGWITGHSYMVYGPLANGATILIHEGIPNFPSPARLGEIVDRHQVNILYTAPTL 360

Query: 361 IRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGG 420
           IRA+MA G    +  DG SLR++GSVGEPINPEAW WY++ +G E CPIVDTWWQTETGG
Sbjct: 361 IRALMAEGKQHFDNFDGKSLRIMGSVGEPINPEAWRWYHEVIGHEHCPIVDTWWQTETGG 420

Query: 421 VLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGD 480
           +LI+PLPGAT  KPGSATRPFFGV PALVDN GN++EGA EGNLV+LDSWPGQ RT+YGD
Sbjct: 421 ILITPLPGATDTKPGSATRPFFGVQPALVDNEGNILEGATEGNLVLLDSWPGQMRTVYGD 480

Query: 481 HDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540
           H+RFV TYFKTF GMYFTGDGARRDEDGYYWITGRVDDV+NVSGHR+GTAE+ESA+VAH 
Sbjct: 481 HERFVLTYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVINVSGHRLGTAEVESALVAHD 540

Query: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAP 600
            VAEAAVVG PHDIKGQGIY YVTL  G E +E LR EL+ WVRKEIG +A+PD+IQWA 
Sbjct: 541 LVAEAAVVGYPHDIKGQGIYAYVTLTKGTEATEELRQELRQWVRKEIGALATPDLIQWAS 600

Query: 601 GLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIET 644
           GLPKTRSGKIMRR LRKIA  E   LGD STLADP V+  LIE+
Sbjct: 601 GLPKTRSGKIMRRFLRKIAANEITNLGDASTLADPSVIDTLIES 644


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: 1440
Number of extensions: 48
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: 650
Length adjustment: 38
Effective length of query: 613
Effective length of database: 612
Effective search space:   375156
Effective search space used:   375156
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 6937938 Sama_2079 (acetyl-CoA synthetase (RefSeq))
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.12219.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 1025.3   0.2          0 1025.1   0.2    1.0  1  lcl|FitnessBrowser__SB2B:6937938  Sama_2079 acetyl-CoA synthetase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SB2B:6937938  Sama_2079 acetyl-CoA synthetase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1025.1   0.2         0         0       3     628 ..      20     643 ..      18     644 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1025.1 bits;  conditional E-value: 0
                         TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdkvai 76 
                                       ++e+y+++y+e++++pe fw+++ak+ ++w+kpf++v+d+s ++    +kWf+dg+ln+s+nc+drh++++ d vai
  lcl|FitnessBrowser__SB2B:6937938  20 NNEQYQKMYQESVANPEGFWGEHAKR-IDWIKPFTQVKDTSYDDqnlYIKWFHDGTLNASANCLDRHLASKGDDVAI 95 
                                       789**********************5.************9987666789**************************** PP

                         TIGR02188  77 iwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaeal 153
                                       iwegd+++e +rk+tY+el++evc++an+lk+ Gvk+gd v+iY+pm++ea++amlacaRiGavhsvvf+Gfs++++
  lcl|FitnessBrowser__SB2B:6937938  96 IWEGDDASE-QRKVTYRELHAEVCQFANALKAEGVKRGDVVTIYMPMVVEATVAMLACARIGAVHSVVFGGFSPDSI 171
                                       *****9985.******************************************************************* PP

                         TIGR02188 154 aeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvwweelvekeasa 229
                                       a+R++d ++kl+itadeg+Rgg++i+lk ++deal++ +  +ve+v+v+krtg  v+ w+egrD+ww+++++ +a +
  lcl|FitnessBrowser__SB2B:6937938 172 ASRVIDGKSKLLITADEGVRGGRKIPLKGNIDEALNRPDVtTVETVIVLKRTGGAVN-WVEGRDKWWHQVTD-GAAT 246
                                       *************************************9988**************66.*************9.6*** PP

                         TIGR02188 230 ecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLan 306
                                       ec++e++++edplf+LYtsGstG+PkGvlhttgGyl++a++t++yvfd+k+++++wCtaDvGW+tGhsY+vygPLan
  lcl|FitnessBrowser__SB2B:6937938 247 ECAVEEMGAEDPLFLLYTSGSTGNPKGVLHTTGGYLVYASMTHEYVFDYKPGEVYWCTADVGWITGHSYMVYGPLAN 323
                                       ***************************************************************************** PP

                         TIGR02188 307 GattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyye 383
                                       Gat l++eg+p++p+++r+ e++++++v+i+YtaPt+iRalm++g++++++ d +slr++gsvGepinpeaw+Wy+e
  lcl|FitnessBrowser__SB2B:6937938 324 GATILIHEGIPNFPSPARLGEIVDRHQVNILYTAPTLIRALMAEGKQHFDNFDGKSLRIMGSVGEPINPEAWRWYHE 400
                                       ***************************************************************************** PP

                         TIGR02188 384 vvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlr 460
                                       v+G+e+cpivdtwWqtetGgilitplpg at++kpgsat+P+fG+++++vd+eg+ +e  +e g Lv+ ++wP+++r
  lcl|FitnessBrowser__SB2B:6937938 401 VIGHEHCPIVDTWWQTETGGILITPLPG-ATDTKPGSATRPFFGVQPALVDNEGNILEGATE-GNLVLLDSWPGQMR 475
                                       ****************************.6****************************8777.79************ PP

                         TIGR02188 461 tiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpd 537
                                       t+ygd+erfv tYfk+++g+yftGDgarrd+dGy+wi+GRvDdvinvsGhrlgtae+esalv+h+ vaeaavvg+p+
  lcl|FitnessBrowser__SB2B:6937938 476 TVYGDHERFVLTYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVINVSGHRLGTAEVESALVAHDLVAEAAVVGYPH 552
                                       ***************************************************************************** PP

                         TIGR02188 538 eikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ellgd 613
                                       +ikg+ i+a+v+l++g+e++e el++el+++vrkeig++a+pd i++++ lPktRsGkimRR+lrkia++e ++lgd
  lcl|FitnessBrowser__SB2B:6937938 553 DIKGQGIYAYVTLTKGTEATE-ELRQELRQWVRKEIGALATPDLIQWASGLPKTRSGKIMRRFLRKIAANEiTNLGD 628
                                       ******************999.5****************************************************** PP

                         TIGR02188 614 vstledpsvveelke 628
                                        stl+dpsv+++l+e
  lcl|FitnessBrowser__SB2B:6937938 629 ASTLADPSVIDTLIE 643
                                       ***********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (650 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.05
# Mc/sec: 8.09
//
[ok]

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

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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, 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

GapMind for catabolism of small carbon sources