Alignments for a candidate for acs in Oleispira antarctica

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Oleispira antarctica

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_046010587.1 OLEAN_RS19275 acetate--CoA ligase

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



>NCBI__GCF_000967895.1:WP_046010587.1
          Length = 656

 Score =  892 bits (2304), Expect = 0.0
 Identities = 424/656 (64%), Positives = 504/656 (76%), Gaps = 5/656 (0%)

Query: 1   MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60
           MS  ++YPV P      L  +  Y+ MYQ S+ +PD FW +QA+RL WI PFT VK  SF
Sbjct: 1   MSEQTVYPVSPAQREKALLTKEQYQVMYQHSLESPDEFWAQQAQRLTWITPFTKVKNVSF 60

Query: 61  DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGD-----DPSESRNITYRELHE 115
           D   + I+WF DG LNVS NC+DRHL ERG + AI+WE D     +  E+R ITY++L  
Sbjct: 61  DKQDLHIRWFEDGFLNVSENCIDRHLVERGHETAILWEPDGENVGEKDEARRITYQQLSS 120

Query: 116 EVCKFANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRI 175
           EV + AN L+   + +GD+VT+Y+PM+PEA +AMLAC RIGA+HSVVF GFSPEALAGRI
Sbjct: 121 EVNRLANGLKSLGIKKGDIVTLYLPMVPEATMAMLACARIGAVHSVVFAGFSPEALAGRI 180

Query: 176 IDCKSKVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDI 235
            D   + VITADEG+R GK +PLK NVD+A+       +  VIV   T G +     RDI
Sbjct: 181 EDGDCRYVITADEGLRGGKHVPLKQNVDEAIALCPAEQVNNVIVLNHTGGEVNHQVGRDI 240

Query: 236 WYEDLMKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDY 295
            Y DL+     VC P+ M AE+ LFILYTSGSTGKPKGV HTT GYLLYA++THE VFDY
Sbjct: 241 DYHDLISQQSDVCPPEPMNAEDPLFILYTSGSTGKPKGVLHTTGGYLLYASMTHEYVFDY 300

Query: 296 KPGEVYWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILY 355
           +PG++YWC ADVGW+TGHSYIVYGPL NGAT ++FEG+P YPDI R A++I+K+K++ILY
Sbjct: 301 RPGDIYWCAADVGWITGHSYIVYGPLCNGATVVMFEGIPTYPDIGRAARLIEKYKINILY 360

Query: 356 TAPTAIRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQ 415
            APTAIR++MA+G AA + +D SSLRLLG+VGEPINP+ W WY++  G+  CPIVDTWWQ
Sbjct: 361 VAPTAIRSLMAAGDAATKNSDLSSLRLLGTVGEPINPDVWRWYHQAFGRGECPIVDTWWQ 420

Query: 416 TETGGVLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQAR 475
           TETG  +I+PLPGAT LKPGSAT P FGV PALVD  G  + GA  GNL+I DSWPGQ R
Sbjct: 421 TETGAAMIAPLPGATDLKPGSATLPMFGVQPALVDEKGIELHGATHGNLIIKDSWPGQMR 480

Query: 476 TLYGDHDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESA 535
           +++GDH RF+DTYF T+ G YFTGDGARRDEDGYYW+TGRVDDVLNVSGHRMGTAEIE+A
Sbjct: 481 SVFGDHQRFIDTYFSTYEGSYFTGDGARRDEDGYYWLTGRVDDVLNVSGHRMGTAEIENA 540

Query: 536 MVAHPKVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDV 595
           +VAH  V EAAVVGVPHDIKG+GIYVYVTL  G E SEALRLEL  WVRKEIGPIA+PD+
Sbjct: 541 LVAHDSVTEAAVVGVPHDIKGEGIYVYVTLGHGFEESEALRLELIKWVRKEIGPIATPDL 600

Query: 596 IQWAPGLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIETHKTMNVA 651
           IQWAP LPKTRSGKIMRRILRKIAT E+D +GD STLADP VV  LI  H  M+ A
Sbjct: 601 IQWAPALPKTRSGKIMRRILRKIATNEFDSIGDTSTLADPSVVDDLIVVHNKMHAA 656


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: 1400
Number of extensions: 63
Number of successful extensions: 2
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: 656
Length adjustment: 38
Effective length of query: 613
Effective length of database: 618
Effective search space:   378834
Effective search space used:   378834
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_046010587.1 OLEAN_RS19275 (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.3695450.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.1e-302  989.4   0.0   3.6e-302  989.2   0.0    1.0  1  NCBI__GCF_000967895.1:WP_046010587.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000967895.1:WP_046010587.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  989.2   0.0  3.6e-302  3.6e-302       4     627 ..      21     647 ..      18     649 .. 0.98

  Alignments for each domain:
  == domain 1  score: 989.2 bits;  conditional E-value: 3.6e-302
                             TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdk 73 
                                            e+y+ +y+++ e+p++fwa++a+ +l+w++pf+kv++ s+++   +++Wfedg lnvs nc+drh+ +r ++
  NCBI__GCF_000967895.1:WP_046010587.1  21 KEQYQVMYQHSLESPDEFWAQQAQ-RLTWITPFTKVKNVSFDKqdlHIRWFEDGFLNVSENCIDRHLVERGHE 92 
                                           789*********************.5*************99887789************************** PP

                             TIGR02188  74 vaiiwegd....eegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhs 142
                                           +ai we d     e++++r++tY++l +ev+rlan lk+lG+kkgd v++Ylpm+pea++amlacaRiGavhs
  NCBI__GCF_000967895.1:WP_046010587.1  93 TAILWEPDgenvGEKDEARRITYQQLSSEVNRLANGLKSLGIKKGDIVTLYLPMVPEATMAMLACARIGAVHS 165
                                           ******997654233489******************************************************* PP

                             TIGR02188 143 vvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkeg 214
                                           vvfaGfs+eala Ri+d ++++vitadeglRggk+++lk++vdea++ +++ +v++v+v+++tg ev+  + g
  NCBI__GCF_000967895.1:WP_046010587.1 166 VVFAGFSPEALAGRIEDGDCRYVITADEGLRGGKHVPLKQNVDEAIALCPAeQVNNVIVLNHTGGEVN-HQVG 237
                                           *************************************************999**************66.999* PP

                             TIGR02188 215 rDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCt 287
                                           rD+ +++l+++ +s+ c+pe++++edplfiLYtsGstGkPkGvlhttgGyll+a++t++yvfd++++di+wC+
  NCBI__GCF_000967895.1:WP_046010587.1 238 RDIDYHDLISQ-QSDVCPPEPMNAEDPLFILYTSGSTGKPKGVLHTTGGYLLYASMTHEYVFDYRPGDIYWCA 309
                                           **********6.************************************************************* PP

                             TIGR02188 288 aDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdl 360
                                           aDvGW+tGhsYivygPL+nGat ++feg+ptypd +r +++iekyk++i+Y+aPtaiR+lm++g++++k+ dl
  NCBI__GCF_000967895.1:WP_046010587.1 310 ADVGWITGHSYIVYGPLCNGATVVMFEGIPTYPDIGRAARLIEKYKINILYVAPTAIRSLMAAGDAATKNSDL 382
                                           ************************************************************************* PP

                             TIGR02188 361 sslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevv 433
                                           sslr+lg+vGepinp+ w+Wy++ +G+++cpivdtwWqtetG+++i+plpg at+lkpgsatlP+fG+++++v
  NCBI__GCF_000967895.1:WP_046010587.1 383 SSLRLLGTVGEPINPDVWRWYHQAFGRGECPIVDTWWQTETGAAMIAPLPG-ATDLKPGSATLPMFGVQPALV 454
                                           ***************************************************.6******************** PP

                             TIGR02188 434 deegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvin 506
                                           de+g e++  ++ g L+ik++wP+++r+++gd++rf++tYf++++g yftGDgarrd+dGy+w++GRvDdv+n
  NCBI__GCF_000967895.1:WP_046010587.1 455 DEKGIELHGATH-GNLIIKDSWPGQMRSVFGDHQRFIDTYFSTYEGSYFTGDGARRDEDGYYWLTGRVDDVLN 526
                                           *******97777.79********************************************************** PP

                             TIGR02188 507 vsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakp 579
                                           vsGhr+gtaeie+alv+h++v+eaavvgvp++ikge i+++v+l +g ee+e +l+ el+k+vrkeigpia+p
  NCBI__GCF_000967895.1:WP_046010587.1 527 VSGHRMGTAEIENALVAHDSVTEAAVVGVPHDIKGEGIYVYVTLGHGFEESE-ALRLELIKWVRKEIGPIATP 598
                                           *************************************************999.6******************* PP

                             TIGR02188 580 dkilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelk 627
                                           d i+++++lPktRsGkimRR+lrkia++e +++gd+stl+dpsvv++l+
  NCBI__GCF_000967895.1:WP_046010587.1 599 DLIQWAPALPKTRSGKIMRRILRKIATNEfDSIGDTSTLADPSVVDDLI 647
                                           *********************************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (656 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 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 16.18
//
[ok]

This GapMind analysis is from Sep 24 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:

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