GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__SB2B:6937938
          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.13354.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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.05
# Mc/sec: 7.03
//
[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:

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