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_046009377.1 OLEAN_RS11725 acetate--CoA ligase

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



>NCBI__GCF_000967895.1:WP_046009377.1
          Length = 653

 Score =  983 bits (2540), Expect = 0.0
 Identities = 465/648 (71%), Positives = 544/648 (83%), Gaps = 5/648 (0%)

Query: 1   MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60
           MS    YPV+  +  +TL +   Y+AMY++S+ + +GFW EQ KR+DWI+PFT V+  SF
Sbjct: 1   MSDIKRYPVKENIGLTTLVNNDQYEAMYKRSIDDSEGFWAEQGKRIDWIEPFTQVRDISF 60

Query: 61  DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKF 120
           D+H V+I W+ DGTLN S NCLDRHLA RGDQ AIIWEGD+P++ R+I+Y+ELH EVC+F
Sbjct: 61  DEHKVNINWYKDGTLNASANCLDRHLATRGDQTAIIWEGDEPTDDRHISYKELHGEVCQF 120

Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180
           ANAL+ Q V +GDVV IYMPM+P+AVVAMLAC RIGAIHSVVFGGFSP+ALAGRI D + 
Sbjct: 121 ANALKTQGVRKGDVVCIYMPMVPQAVVAMLACARIGAIHSVVFGGFSPDALAGRIDDSQV 180

Query: 181 KVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDL 240
           KVVITADEGVR GK +PLK NVD+ALT+P  ++++KVIV KRT  NI W++ RDIWY D 
Sbjct: 181 KVVITADEGVRGGKTVPLKENVDEALTHPSVNTVEKVIVVKRTGANIDWHRSRDIWYHDA 240

Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEV 300
           +      C P EM AE+ LFILYTSGSTGKPKGV HTT GY++YA+LTHE VFDY+ GEV
Sbjct: 241 IAKESKHCQPAEMRAEDPLFILYTSGSTGKPKGVVHTTGGYMVYASLTHEYVFDYQEGEV 300

Query: 301 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTA 360
           YWCTADVGW+TGH+Y+VYGPLANGAT+L+ EG+PNYP+I RV++V+DKH V+ILYTAPTA
Sbjct: 301 YWCTADVGWITGHTYLVYGPLANGATSLMCEGLPNYPNINRVSQVVDKHGVNILYTAPTA 360

Query: 361 IRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGG 420
           IRA+MA G AAV      SLR+LG+VGEPINPEAW+WYY+ +G+ERCPIVDTWWQTETGG
Sbjct: 361 IRALMAEGDAAVTETKRHSLRVLGTVGEPINPEAWEWYYRTIGEERCPIVDTWWQTETGG 420

Query: 421 VLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGD 480
           ++I+PLPGAT LKPGSATRPFFGV PALVD  GN++EG  EGNLVILDSWPGQ+RTLYGD
Sbjct: 421 IMITPLPGATTLKPGSATRPFFGVQPALVDAEGNIVEGVGEGNLVILDSWPGQSRTLYGD 480

Query: 481 HDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540
           H+RF+ TYF T++GMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESA+VAHP
Sbjct: 481 HERFMQTYFSTYAGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESALVAHP 540

Query: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNAGE-----ETSEALRLELKNWVRKEIGPIASPDV 595
           KVAEAAVVG PHDIKGQGIYVYVTLN GE     E ++AL LELK WVR++IGPIA+PD+
Sbjct: 541 KVAEAAVVGYPHDIKGQGIYVYVTLNKGELSADKEVNDALVLELKKWVRQDIGPIATPDL 600

Query: 596 IQWAPGLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIE 643
           IQ   GLPKTRSGKIMRRILRKIA  E   LGD STLADP VV  LIE
Sbjct: 601 IQLTSGLPKTRSGKIMRRILRKIAENECGALGDTSTLADPAVVDELIE 648


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: 1419
Number of extensions: 59
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: 653
Length adjustment: 38
Effective length of query: 613
Effective length of database: 615
Effective search space:   376995
Effective search space used:   376995
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_046009377.1 OLEAN_RS11725 (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.3694477.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 1018.6   0.6          0 1018.4   0.6    1.0  1  NCBI__GCF_000967895.1:WP_046009377.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000967895.1:WP_046009377.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1018.4   0.6         0         0       3     628 ..      20     648 ..      18     649 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1018.4 bits;  conditional E-value: 0
                             TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkd 72 
                                           ++++y+++y+++i+d e fwa+++k +++w++pf++v+d s+++   +++W++dg+ln+s+nc+drh+++r d
  NCBI__GCF_000967895.1:WP_046009377.1  20 NNDQYEAMYKRSIDDSEGFWAEQGK-RIDWIEPFTQVRDISFDEhkvNINWYKDGTLNASANCLDRHLATRGD 91 
                                           789**********************.5************9998777899************************ PP

                             TIGR02188  73 kvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvf 145
                                           ++aiiwegde++ d r+++Y+el+ evc++an+lk++Gv+kgd v+iY+pm+p+av+amlacaRiGa+hsvvf
  NCBI__GCF_000967895.1:WP_046009377.1  92 QTAIIWEGDEPT-DDRHISYKELHGEVCQFANALKTQGVRKGDVVCIYMPMVPQAVVAMLACARIGAIHSVVF 163
                                           **********99.5*********************************************************** PP

                             TIGR02188 146 aGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDv 217
                                           +Gfs++ala Ri d++ k+vitadeg+Rggk+++lk++vdeal++ +  +vekv+vvkrtg+++  w+ +rD+
  NCBI__GCF_000967895.1:WP_046009377.1 164 GGFSPDALAGRIDDSQVKVVITADEGVRGGKTVPLKENVDEALTHPSVnTVEKVIVVKRTGANID-WHRSRDI 235
                                           *********************************************9988**************66.******* PP

                             TIGR02188 218 wweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDv 290
                                           w++++++k +s++c+p+++ +edplfiLYtsGstGkPkGv+httgGy+++a+lt++yvfd+++++++wCtaDv
  NCBI__GCF_000967895.1:WP_046009377.1 236 WYHDAIAK-ESKHCQPAEMRAEDPLFILYTSGSTGKPKGVVHTTGGYMVYASLTHEYVFDYQEGEVYWCTADV 307
                                           *******7.**************************************************************** PP

                             TIGR02188 291 GWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlssl 363
                                           GW+tGh+Y+vygPLanGat+l+ eg p+yp+ +r+ +v++k++v+i+YtaPtaiRalm++g+++v++++++sl
  NCBI__GCF_000967895.1:WP_046009377.1 308 GWITGHTYLVYGPLANGATSLMCEGLPNYPNINRVSQVVDKHGVNILYTAPTAIRALMAEGDAAVTETKRHSL 380
                                           ************************************************************************* PP

                             TIGR02188 364 rvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdee 436
                                           rvlg+vGepinpeaweWyy+++G+e+cpivdtwWqtetGgi+itplpg at lkpgsat+P+fG+++++vd e
  NCBI__GCF_000967895.1:WP_046009377.1 381 RVLGTVGEPINPEAWEWYYRTIGEERCPIVDTWWQTETGGIMITPLPG-ATTLKPGSATRPFFGVQPALVDAE 452
                                           ************************************************.6*********************** PP

                             TIGR02188 437 gkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsG 509
                                           g+ ve   e g Lvi ++wP++ rt+ygd+erf++tYf+++ g+yftGDgarrd+dGy+wi+GRvDdv+nvsG
  NCBI__GCF_000967895.1:WP_046009377.1 453 GNIVEGVGE-GNLVILDSWPGQSRTLYGDHERFMQTYFSTYAGMYFTGDGARRDEDGYYWITGRVDDVLNVSG 524
                                           ****96666.78************************************************************* PP

                             TIGR02188 510 hrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedee....elekelkklvrkeigpiak 578
                                           hr+gtaeiesalv+h++vaeaavvg+p++ikg+ i+++v+l++g+ + ++    +l  elkk+vr+ igpia+
  NCBI__GCF_000967895.1:WP_046009377.1 525 HRMGTAEIESALVAHPKVAEAAVVGYPHDIKGQGIYVYVTLNKGELSADKevndALVLELKKWVRQDIGPIAT 597
                                           *****************************************99876555535567899*************** PP

                             TIGR02188 579 pdkilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                           pd i++++ lPktRsGkimRR+lrkiae+e  +lgd+stl+dp+vv+el+e
  NCBI__GCF_000967895.1:WP_046009377.1 598 PDLIQLTSGLPKTRSGKIMRRILRKIAENEcGALGDTSTLADPAVVDELIE 648
                                           ******************************99****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (653 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: 00:00:00.01
# Mc/sec: 22.32
//
[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