Alignments for a candidate for acs in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Shewanella oneidensis MR-1

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate 201881 SO2743 acetyl-coenzyme A synthetase (NCBI ptt file)

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



>FitnessBrowser__MR1:201881
          Length = 650

 Score =  986 bits (2548), Expect = 0.0
 Identities = 456/649 (70%), Positives = 540/649 (83%)

Query: 1   MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60
           MS+ SLY V   +AA+ L +   YK MYQ+S+VNP+GFWRE  KR+DWIKP+T +K+T+F
Sbjct: 1   MSSQSLYKVSGNIAANALVNNDQYKTMYQESIVNPEGFWREHGKRIDWIKPYTKIKKTTF 60

Query: 61  DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKF 120
           DDH++ I WF DGTLN S NCLDRHLA   D++AIIWEGD+ +E R ITY ELH +VCKF
Sbjct: 61  DDHNLSINWFYDGTLNASANCLDRHLAAHSDRVAIIWEGDNANEQRKITYGELHTQVCKF 120

Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180
           ANALR Q V RGD+VTIYMPM+PEA VAMLAC RIGA+HSVVFGGFSP+++A R+ID KS
Sbjct: 121 ANALRSQGVRRGDIVTIYMPMVPEAAVAMLACARIGAVHSVVFGGFSPDSIASRVIDGKS 180

Query: 181 KVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDL 240
           K+VIT+DEG+R G+ IPLK N+DDAL +P+ +S++KVIV KRT G I W + RD+W+  L
Sbjct: 181 KIVITSDEGMRGGRAIPLKRNIDDALKHPDVTSVEKVIVLKRTGGKIDWVEGRDVWWHSL 240

Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEV 300
           ++ A   CA +EMGAE+ LF+LYTSGSTG PKGV HTT GY++YA++THE VFDYKPGE+
Sbjct: 241 VETASEHCAVEEMGAEDPLFLLYTSGSTGNPKGVLHTTGGYMVYASMTHEYVFDYKPGEI 300

Query: 301 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTA 360
           YWCTADVGW+TGHSY+VYGPLANGAT L+ EGVPN+P   R+ ++ID+HKV+ILYTAPT 
Sbjct: 301 YWCTADVGWITGHSYMVYGPLANGATVLIHEGVPNHPSPARLGEMIDRHKVNILYTAPTL 360

Query: 361 IRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGG 420
           IRA+MA G    +  +GSSLR++GSVGEPINPEAW WY++ +G E CPIVDTWWQTETGG
Sbjct: 361 IRALMAEGKQHFDKYNGSSLRIMGSVGEPINPEAWRWYHEVIGHEHCPIVDTWWQTETGG 420

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

Query: 481 HDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540
           H+RFV TYFKTF GMYFTGDGARRDEDGYYWITGRVDDV+NVSGHR+GTAE+ESA+V+H 
Sbjct: 481 HERFVLTYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVINVSGHRLGTAEVESALVSHE 540

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

Query: 601 GLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIETHKTMN 649
           GLPKTRSGKIMRR LRKIA  E   LGD STLADP V+  LIET    N
Sbjct: 601 GLPKTRSGKIMRRFLRKIAANEVTNLGDASTLADPAVIETLIETRLNRN 649


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: 1457
Number of extensions: 51
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 201881 SO2743 (acetyl-coenzyme A synthetase (NCBI ptt file))
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.13640.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 1036.4   0.3          0 1036.2   0.3    1.0  1  lcl|FitnessBrowser__MR1:201881  SO2743 acetyl-coenzyme A synthet


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:201881  SO2743 acetyl-coenzyme A synthetase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1036.2   0.3         0         0       3     628 ..      20     643 ..      18     644 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1036.2 bits;  conditional E-value: 0
                       TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdkvaiiw 78 
                                     ++++yk++y+e+i +pe fw++++k +++w+kp++k++++++++   +++Wf dg+ln+s+nc+drh+++++d+vaiiw
  lcl|FitnessBrowser__MR1:201881  20 NNDQYKTMYQESIVNPEGFWREHGK-RIDWIKPYTKIKKTTFDDhnlSINWFYDGTLNASANCLDRHLAAHSDRVAIIW 97 
                                     789**********************.5************998876789******************************* PP

                       TIGR02188  79 egdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaealaeRi 157
                                     egd+++e +rk+tY el+++vc++an+l+++Gv++gd v+iY+pm+pea++amlacaRiGavhsvvf+Gfs++++a+R+
  lcl|FitnessBrowser__MR1:201881  98 EGDNANE-QRKITYGELHTQVCKFANALRSQGVRRGDIVTIYMPMVPEAAVAMLACARIGAVHSVVFGGFSPDSIASRV 175
                                     ***9885.*********************************************************************** PP

                       TIGR02188 158 vdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvwweelvekeasaecepek 235
                                     +d ++k+vit+deg+Rgg++i+lk+++d+al++ +  svekv+v+krtg ++  w+egrDvww++lve+ as++c++e+
  lcl|FitnessBrowser__MR1:201881 176 IDGKSKIVITSDEGMRGGRAIPLKRNIDDALKHPDVtSVEKVIVLKRTGGKID-WVEGRDVWWHSLVET-ASEHCAVEE 252
                                     *********************************9999**************66.**************6.********* PP

                       TIGR02188 236 ldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanGattllfe 314
                                     +++edplf+LYtsGstG+PkGvlhttgGy+++a++t++yvfd+k+++i+wCtaDvGW+tGhsY+vygPLanGat l++e
  lcl|FitnessBrowser__MR1:201881 253 MGAEDPLFLLYTSGSTGNPKGVLHTTGGYMVYASMTHEYVFDYKPGEIYWCTADVGWITGHSYMVYGPLANGATVLIHE 331
                                     ******************************************************************************* PP

                       TIGR02188 315 gvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpiv 393
                                     gvp++p+++r+ e+i+++kv+i+YtaPt+iRalm++g+++++k++ sslr++gsvGepinpeaw+Wy+ev+G+e+cpiv
  lcl|FitnessBrowser__MR1:201881 332 GVPNHPSPARLGEMIDRHKVNILYTAPTLIRALMAEGKQHFDKYNGSSLRIMGSVGEPINPEAWRWYHEVIGHEHCPIV 410
                                     ******************************************************************************* PP

                       TIGR02188 394 dtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvet 472
                                     dtwWqtetGgilitplpg at++kpgsat+P+fG+++++vd+ g+ +e  +e g Lv+ ++wP+++rt+ygd+erfv t
  lcl|FitnessBrowser__MR1:201881 411 DTWWQTETGGILITPLPG-ATDTKPGSATRPFFGVQPALVDNMGNILEGATE-GNLVLLDSWPGQMRTVYGDHERFVLT 487
                                     ******************.6****************************8777.79************************ PP

                       TIGR02188 473 YfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlk 551
                                     Yfk+++g+yftGDgarrd+dGy+wi+GRvDdvinvsGhrlgtae+esalvshe vaeaavvg+p++ikg+ i+a+v+l+
  lcl|FitnessBrowser__MR1:201881 488 YFKTFRGMYFTGDGARRDEDGYYWITGRVDDVINVSGHRLGTAEVESALVSHELVAEAAVVGYPHDIKGQGIYAYVTLT 566
                                     ******************************************************************************* PP

                       TIGR02188 552 egveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                     +g+ee+e el++el+++vrkeig++a+pd i++++ lPktRsGkimRR+lrkia++e ++lgd stl+dp+v+e+l+e
  lcl|FitnessBrowser__MR1:201881 567 RGTEESE-ELRQELRQWVRKEIGALATPDLIQWATGLPKTRSGKIMRRFLRKIAANEvTNLGDASTLADPAVIETLIE 643
                                     ****999.5*****************************************************************9987 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 12.04
//
[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)
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