Alignments for a candidate for acs in Dokdonella koreensis DS-123

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Dokdonella koreensis DS-123

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_067642555.1 I596_RS00340 acetate--CoA ligase

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



>NCBI__GCF_001632775.1:WP_067642555.1
          Length = 646

 Score =  901 bits (2329), Expect = 0.0
 Identities = 428/637 (67%), Positives = 503/637 (78%)

Query: 6   LYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHV 65
           L+PV    AA    D A Y+  Y +SV +P  FW    +RLDWI P+T VK  S+D   +
Sbjct: 4   LHPVPDTFAAHARIDRAQYETAYAESVKDPAAFWDRIGRRLDWITPYTQVKDVSYDARDL 63

Query: 66  DIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANALR 125
            I+W+ DG LNVS NCLDRHLA RGD+ AIIWEGDDP+ESR ++YRELH EVCK AN L 
Sbjct: 64  HIRWYYDGELNVSANCLDRHLAARGDKTAIIWEGDDPAESRRVSYRELHAEVCKAANLLT 123

Query: 126 GQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVIT 185
              + + D V IY+PMIPEA VAMLACTRIGAIH++VF GFSP++LA RI D + K+VIT
Sbjct: 124 SLGIRKDDRVAIYLPMIPEAAVAMLACTRIGAIHTIVFAGFSPDSLASRIADSQCKLVIT 183

Query: 186 ADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKVAG 245
           ADEG+R  KK+PLKANVD+AL  P T+S++ V+V +RT G I     RD W+  L+    
Sbjct: 184 ADEGLRGKKKVPLKANVDEALKRPNTNSVETVLVVRRTGGAIDMQVPRDRWWHALLADQP 243

Query: 246 TVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWCTA 305
              AP    AE  LFILYTSGSTG PKGV HTT GYL+YA+ THE VFD +  +VYWCTA
Sbjct: 244 ATHAPVACEAEHPLFILYTSGSTGTPKGVLHTTGGYLVYASFTHEAVFDLREDDVYWCTA 303

Query: 306 DVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRAMM 365
           D+GWVTGHSY++YGPLANGATT++FEGVPN+PD +R  +V+DKHKV++ YTAPTAIRA+M
Sbjct: 304 DIGWVTGHSYLIYGPLANGATTVMFEGVPNFPDSSRFWQVVDKHKVTLFYTAPTAIRALM 363

Query: 366 ASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLISP 425
             G   V     +SLRLLGSVGEPINPEAW+WYY+ VG  RCPIVDTWWQTETGG+LI+P
Sbjct: 364 REGEDPVRKTSRASLRLLGSVGEPINPEAWEWYYRVVGDSRCPIVDTWWQTETGGILITP 423

Query: 426 LPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDRFV 485
           LPGAT LKPGSAT PFFG+ P +VD  G ++EGAAEGNLV+ DSWPGQ RT+YGDH RF+
Sbjct: 424 LPGATDLKPGSATLPFFGITPQIVDANGAVLEGAAEGNLVLTDSWPGQMRTVYGDHQRFI 483

Query: 486 DTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAEA 545
           DTYF+T+ G YFTGDGARRDEDGYYWITGRVDDV+NVSGHR+GTAE+ESA+VAHP+VAEA
Sbjct: 484 DTYFRTYPGTYFTGDGARRDEDGYYWITGRVDDVINVSGHRLGTAEVESALVAHPQVAEA 543

Query: 546 AVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLPKT 605
           AVVG PHDIKGQGIY YVTL  G E ++ALR EL  WVRKEIGPIA+PD +QWAPGLPKT
Sbjct: 544 AVVGCPHDIKGQGIYAYVTLKTGVEPTDALRKELVAWVRKEIGPIATPDHLQWAPGLPKT 603

Query: 606 RSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLI 642
           RSGKIMRRILRKIA  + D LGD STLADP VVA+L+
Sbjct: 604 RSGKIMRRILRKIAENQPDALGDTSTLADPSVVANLV 640


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: 1370
Number of extensions: 52
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 WP_067642555.1 I596_RS00340 (acetate--CoA ligase)
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.356366.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 1024.7   0.0          0 1024.5   0.0    1.0  1  NCBI__GCF_001632775.1:WP_067642555.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001632775.1:WP_067642555.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1024.5   0.0         0         0       4     628 ..      19     641 ..      16     642 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1024.5 bits;  conditional E-value: 0
                             TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdk 73 
                                             +y++ y+e+++dp++fw++ ++ +l+w++p+++v+d s ++   +++W+ dgelnvs+nc+drh+++r dk
  NCBI__GCF_001632775.1:WP_067642555.1  19 RAQYETAYAESVKDPAAFWDRIGR-RLDWITPYTQVKDVSYDArdlHIRWYYDGELNVSANCLDRHLAARGDK 90 
                                           579*********************.5************998777789************************** PP

                             TIGR02188  74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146
                                           +aiiwegd++ e sr+++Y+el++evc++an+l++lG++k+drvaiYlpmipea++amlac+RiGa+h++vfa
  NCBI__GCF_001632775.1:WP_067642555.1  91 TAIIWEGDDPAE-SRRVSYRELHAEVCKAANLLTSLGIRKDDRVAIYLPMIPEAAVAMLACTRIGAIHTIVFA 162
                                           **********96.************************************************************ PP

                             TIGR02188 147 GfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvw 218
                                           Gfs+++la+Ri d+++klvitadeglRg+k+++lk++vdeal++ ++ sve+vlvv+rtg  +  ++  rD w
  NCBI__GCF_001632775.1:WP_067642555.1 163 GFSPDSLASRIADSQCKLVITADEGLRGKKKVPLKANVDEALKRPNTnSVETVLVVRRTGGAID-MQVPRDRW 234
                                           ********************************************9988**************66.******** PP

                             TIGR02188 219 weelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvG 291
                                           w+ l+++ ++a+++p + ++e+plfiLYtsGstG+PkGvlhttgGyl++a+ t++ vfd++++d++wCtaD+G
  NCBI__GCF_001632775.1:WP_067642555.1 235 WHALLAD-QPATHAPVACEAEHPLFILYTSGSTGTPKGVLHTTGGYLVYASFTHEAVFDLREDDVYWCTADIG 306
                                           ******7.***************************************************************** PP

                             TIGR02188 292 WvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslr 364
                                           WvtGhsY++ygPLanGatt++fegvp++pd+srfw+v++k+kvt fYtaPtaiRalm++ge+ v+k+++ slr
  NCBI__GCF_001632775.1:WP_067642555.1 307 WVTGHSYLIYGPLANGATTVMFEGVPNFPDSSRFWQVVDKHKVTLFYTAPTAIRALMREGEDPVRKTSRASLR 379
                                           ************************************************************************* PP

                             TIGR02188 365 vlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeeg 437
                                           +lgsvGepinpeaweWyy+vvG+++cpivdtwWqtetGgilitplpg at+lkpgsatlP+fGi++++vd +g
  NCBI__GCF_001632775.1:WP_067642555.1 380 LLGSVGEPINPEAWEWYYRVVGDSRCPIVDTWWQTETGGILITPLPG-ATDLKPGSATLPFFGITPQIVDANG 451
                                           ***********************************************.6************************ PP

                             TIGR02188 438 keveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGh 510
                                             +e  +e g Lv++++wP+++rt+ygd++rf++tYf++++g+yftGDgarrd+dGy+wi+GRvDdvinvsGh
  NCBI__GCF_001632775.1:WP_067642555.1 452 AVLEGAAE-GNLVLTDSWPGQMRTVYGDHQRFIDTYFRTYPGTYFTGDGARRDEDGYYWITGRVDDVINVSGH 523
                                           ****8777.79************************************************************** PP

                             TIGR02188 511 rlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkil 583
                                           rlgtae+esalv+h++vaeaavvg p++ikg+ i+a+v+lk+gve+++ +l+kel ++vrkeigpia+pd+++
  NCBI__GCF_001632775.1:WP_067642555.1 524 RLGTAEVESALVAHPQVAEAAVVGCPHDIKGQGIYAYVTLKTGVEPTD-ALRKELVAWVRKEIGPIATPDHLQ 595
                                           ************************************************.5*********************** PP

                             TIGR02188 584 vveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                           +++ lPktRsGkimRR+lrkiae++ ++lgd+stl+dpsvv++l +
  NCBI__GCF_001632775.1:WP_067642555.1 596 WAPGLPKTRSGKIMRRILRKIAENQpDALGDTSTLADPSVVANLVN 641
                                           *****************************************99865 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 22.71
//
[ok]

This GapMind analysis is from Sep 24 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