Alignments for a candidate for acs in Brucella microti CCM 4915

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Brucella microti CCM 4915

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate WP_002964888.1 BMI_RS08370 acetate--CoA ligase

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



>NCBI__GCF_000022745.1:WP_002964888.1
          Length = 651

 Score =  900 bits (2326), Expect = 0.0
 Identities = 431/645 (66%), Positives = 503/645 (77%), Gaps = 5/645 (0%)

Query: 6   LYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHV 65
           LYPV PE   +TL D  TY   Y++SV +PDGFW +  +R+DW KPFT VK T F+   V
Sbjct: 5   LYPVLPEAKKNTLIDNETYLEWYEESVSDPDGFWAKHGRRIDWFKPFTKVKNTDFNGD-V 63

Query: 66  DIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANALR 125
            IKW+ DG  NVSYNC+DRHL  RGD++AIIWEGD+P   + ITYREL+E VC+ AN L+
Sbjct: 64  TIKWYEDGVTNVSYNCIDRHLKSRGDKVAIIWEGDNPYIDKKITYRELYENVCRMANVLK 123

Query: 126 GQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVIT 185
              V +GD VTIY+PMIPEA  AMLAC RIGA+HSVVF GFSPEALAGRI+DC+S  VIT
Sbjct: 124 KHGVKKGDRVTIYLPMIPEAAYAMLACARIGAVHSVVFAGFSPEALAGRIVDCESTFVIT 183

Query: 186 ADEGVRAGKKIPLKANVDDAL--TNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKV 243
           ADEGVR GK + LK N D A+     +   + KV+V +RT G + W + RD+WY   +  
Sbjct: 184 ADEGVRGGKPVALKENTDTAIDIAAKQYVMVNKVLVVRRTGGKVSWGRGRDLWYHQEVAS 243

Query: 244 AGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWC 303
               C P+ M AE+ LFILYTSGSTGKPKGV HTT GYL+YA++TH+ VFDY  GE+YWC
Sbjct: 244 VEPHCEPEPMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYASMTHQYVFDYHDGEIYWC 303

Query: 304 TADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRA 363
           TADVGWVTGHSYIVYGPLANGATTL+FEGVPN+PD  R  +V+DKH V+I YTAPTA+RA
Sbjct: 304 TADVGWVTGHSYIVYGPLANGATTLMFEGVPNFPDQGRFWEVVDKHHVNIFYTAPTALRA 363

Query: 364 MMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLI 423
           +M +G   V  +  S+LRLLGSVGEPINPEAW+WYY  VG ++CPIVDTWWQTE GG+LI
Sbjct: 364 LMGAGDEFVTRSSRSTLRLLGSVGEPINPEAWEWYYNVVGDQKCPIVDTWWQTENGGILI 423

Query: 424 SPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDR 483
           +PLPGAT LKPGSATRPFFGV P LVDN GN+ EG A+GNL I DSWPGQ RT+YGDH R
Sbjct: 424 TPLPGATDLKPGSATRPFFGVKPVLVDNEGNVQEGVADGNLCISDSWPGQMRTVYGDHKR 483

Query: 484 FVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVA 543
           F++TYF T+ GMYF+GDG RRDEDGYYWITGRVDDVLN+SGHR+GTAEIESA+V+H  V+
Sbjct: 484 FIETYFSTYKGMYFSGDGCRRDEDGYYWITGRVDDVLNISGHRLGTAEIESALVSHHSVS 543

Query: 544 EAAVVGVPHDIKGQGIYVYVTLNAGEETS--EALRLELKNWVRKEIGPIASPDVIQWAPG 601
           EAAVVG PH IKGQGIY YVTL  G +    + LR EL   VRKEIGPIA+PD IQ+APG
Sbjct: 544 EAAVVGYPHPIKGQGIYCYVTLMTGADAQDPDELRKELVQHVRKEIGPIATPDKIQFAPG 603

Query: 602 LPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIETHK 646
           LPKTRSGKIMRRILRKIA  E+  LGD STLADPGVV  LIE  +
Sbjct: 604 LPKTRSGKIMRRILRKIAEDEFGALGDTSTLADPGVVDDLIENRQ 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: 1475
Number of extensions: 65
Number of successful extensions: 4
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: 651
Length adjustment: 38
Effective length of query: 613
Effective length of database: 613
Effective search space:   375769
Effective search space used:   375769
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_002964888.1 BMI_RS08370 (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.1244023.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 1041.1   0.0          0 1040.9   0.0    1.0  1  NCBI__GCF_000022745.1:WP_002964888.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000022745.1:WP_002964888.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1040.9   0.0         0         0       3     628 ..      19     645 ..      17     646 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1040.9 bits;  conditional E-value: 0
                             TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep..kvkWfedgelnvsyncvdrhvekrkdk 73 
                                           ++e+y e+yee+++dp+ fwak+++ +++w+kpf+kv++++++   ++kW+edg +nvsync+drh+++r dk
  NCBI__GCF_000022745.1:WP_002964888.1  19 DNETYLEWYEESVSDPDGFWAKHGR-RIDWFKPFTKVKNTDFNGdvTIKWYEDGVTNVSYNCIDRHLKSRGDK 90 
                                           6789*********************.5**************9987899************************* PP

                             TIGR02188  74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146
                                           vaiiwegd++    +k+tY+el+++vcr+anvlk++Gvkkgdrv+iYlpmipea++amlacaRiGavhsvvfa
  NCBI__GCF_000022745.1:WP_002964888.1  91 VAIIWEGDNPYI-DKKITYRELYENVCRMANVLKKHGVKKGDRVTIYLPMIPEAAYAMLACARIGAVHSVVFA 162
                                           ********9996.9*********************************************************** PP

                             TIGR02188 147 GfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee...svekvlvvkrtgeevaewkegrD 216
                                           Gfs+eala Rivd+e+ +vitadeg+Rggk ++lk+++d a++ a +   +v+kvlvv+rtg +v+ w  grD
  NCBI__GCF_000022745.1:WP_002964888.1 163 GFSPEALAGRIVDCESTFVITADEGVRGGKPVALKENTDTAIDIAAKqyvMVNKVLVVRRTGGKVS-WGRGRD 234
                                           ******************************************977665679*************76.****** PP

                             TIGR02188 217 vwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaD 289
                                           +w++++v++ ++ +cepe++++edplfiLYtsGstGkPkGvlhttgGyl++a++t++yvfd++d++i+wCtaD
  NCBI__GCF_000022745.1:WP_002964888.1 235 LWYHQEVAS-VEPHCEPEPMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYASMTHQYVFDYHDGEIYWCTAD 306
                                           ********6.*************************************************************** PP

                             TIGR02188 290 vGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlss 362
                                           vGWvtGhsYivygPLanGattl+fegvp++pd++rfwev++k++v+ifYtaPta+Ralm +g+e+v++ ++s+
  NCBI__GCF_000022745.1:WP_002964888.1 307 VGWVTGHSYIVYGPLANGATTLMFEGVPNFPDQGRFWEVVDKHHVNIFYTAPTALRALMGAGDEFVTRSSRST 379
                                           ************************************************************************* PP

                             TIGR02188 363 lrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvde 435
                                           lr+lgsvGepinpeaweWyy+vvG++kcpivdtwWqte Ggilitplpg at+lkpgsat+P+fG+++++vd+
  NCBI__GCF_000022745.1:WP_002964888.1 380 LRLLGSVGEPINPEAWEWYYNVVGDQKCPIVDTWWQTENGGILITPLPG-ATDLKPGSATRPFFGVKPVLVDN 451
                                           *************************************************.6********************** PP

                             TIGR02188 436 egkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvs 508
                                           eg+  e  ++ g L+i+++wP+++rt+ygd++rf+etYf+++kg+yf+GDg+rrd+dGy+wi+GRvDdv+n+s
  NCBI__GCF_000022745.1:WP_002964888.1 452 EGNVQEGVAD-GNLCISDSWPGQMRTVYGDHKRFIETYFSTYKGMYFSGDGCRRDEDGYYWITGRVDDVLNIS 523
                                           **98886666.89************************************************************ PP

                             TIGR02188 509 Ghrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedee.elekelkklvrkeigpiakpd 580
                                           Ghrlgtaeiesalvsh++v+eaavvg+p+ ikg+ i+++v+l++g+++++  el+kel ++vrkeigpia+pd
  NCBI__GCF_000022745.1:WP_002964888.1 524 GHRLGTAEIESALVSHHSVSEAAVVGYPHPIKGQGIYCYVTLMTGADAQDPdELRKELVQHVRKEIGPIATPD 596
                                           *******************************************9988655339******************** PP

                             TIGR02188 581 kilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                           ki++++ lPktRsGkimRR+lrkiae+e  +lgd+stl+dp vv++l+e
  NCBI__GCF_000022745.1:WP_002964888.1 597 KIQFAPGLPKTRSGKIMRRILRKIAEDEfGALGDTSTLADPGVVDDLIE 645
                                           *********************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (651 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: 21.61
//
[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 2024 update 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