Alignments for a candidate for acs in Rhizobium leguminosarum bv. trifolii WSM1325

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Rhizobium leguminosarum bv. trifolii WSM1325

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_012759526.1 RLEG_RS21015 acetate--CoA ligase

Query= SwissProt::P27550
         (652 letters)



>NCBI__GCF_000023185.1:WP_012759526.1
          Length = 651

 Score =  880 bits (2273), Expect = 0.0
 Identities = 422/633 (66%), Positives = 494/633 (78%), Gaps = 3/633 (0%)

Query: 16  RCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVSIKWYEDGTL 75
           R LI+ ++Y   Y++S+  PD FWG+ GK +DW KPY KVKNTSF  G VSIKW+EDG  
Sbjct: 15  RALIDKEKYLKWYEESVENPDKFWGKHGKRIDWFKPYTKVKNTSFT-GKVSIKWFEDGQT 73

Query: 76  NLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRFANTLLELGIKKGDVV 135
           N++ NC+DRHL+ NGD+ AIIWEGD+    K ++Y EL+  VCR AN L + G+KKGD V
Sbjct: 74  NVSYNCIDRHLKTNGDQVAIIWEGDNPYIDKKVTYNELYEHVCRMANVLKKHGVKKGDRV 133

Query: 136 AIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDEGVRAGRS 195
            IYMPM+PEAA AMLACARIGAVHSV+FGGFSPEA+AGRI+D  S  VIT DEG+R G+ 
Sbjct: 134 TIYMPMIPEAAYAMLACARIGAVHSVVFGGFSPEALAGRIVDCESTFVITCDEGLRGGKP 193

Query: 196 IPLKKNVDDALKNP--NVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASDQHQAEEM 253
           +PLK N D A+         VE V+V++RTGGK  W  GRDLW H  +     +    +M
Sbjct: 194 VPLKNNTDTAIDIAARQHVIVEKVLVVRRTGGKTGWAPGRDLWHHQEIATVKAECPPVKM 253

Query: 254 NAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVGWVTGH 313
            AEDPLFILYTSGSTGKPKGVLHTTGGYLVYAA+T +YVFDYH GD+YWCTADVGWVTGH
Sbjct: 254 KAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAAMTHEYVFDYHHGDVYWCTADVGWVTGH 313

Query: 314 SYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEGDKAIE 373
           SY+LYGPLA  ATTLMFEGVPN+P   R  +V+DKH+VNI YTAPTAIR+LM  GD  + 
Sbjct: 314 SYILYGPLANCATTLMFEGVPNFPDQGRFWEVIDKHKVNIFYTAPTAIRSLMGAGDDFVT 373

Query: 374 GTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPGATELK 433
            + RSSLR+LG+VGEPINPEAWEWY+  +G+++CPV+DTWWQTETGG MITPLPGAT+LK
Sbjct: 374 RSSRSSLRLLGTVGEPINPEAWEWYYNVVGDKRCPVIDTWWQTETGGHMITPLPGATDLK 433

Query: 434 AGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHERFEQTYFSTFK 493
            GSAT PFFGV+P LVDNEG  LEG  +G+L ITDSWPGQ RT++GDHERF QTYFST+K
Sbjct: 434 PGSATTPFFGVKPQLVDNEGKVLEGPADGNLCITDSWPGQMRTVYGDHERFIQTYFSTYK 493

Query: 494 NMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHN 553
             YF+GDG RRD DGYYWITGRVDDVLNVSGHRLGTAE+ESALV+H  ++EAAVVG PH 
Sbjct: 494 GKYFTGDGCRRDADGYYWITGRVDDVLNVSGHRLGTAEVESALVSHNLVSEAAVVGYPHP 553

Query: 554 IKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRR 613
           IKGQ IY YVTL  G E S  L  E+   VR EIGP+A PD + +   LPKTRSGKIMRR
Sbjct: 554 IKGQGIYCYVTLMAGHEGSDTLRQELVKHVRGEIGPIAAPDKIQFAPGLPKTRSGKIMRR 613

Query: 614 ILRKIAAGDTSNLGDTSTLADPGVVEKLLEEKQ 646
           ILRKIA  D   LGDTSTLADP VV+ L+  +Q
Sbjct: 614 ILRKIAEDDFGALGDTSTLADPAVVDDLIANRQ 646


Lambda     K      H
   0.317    0.135    0.421 

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: 1488
Number of extensions: 57
Number of successful extensions: 3
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: 652
Length of database: 651
Length adjustment: 38
Effective length of query: 614
Effective length of database: 613
Effective search space:   376382
Effective search space used:   376382
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_012759526.1 RLEG_RS21015 (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.925591.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 1032.6   0.0          0 1032.4   0.0    1.0  1  NCBI__GCF_000023185.1:WP_012759526.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000023185.1:WP_012759526.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1032.4   0.0         0         0       3     628 ..      19     643 ..      17     644 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1032.4 bits;  conditional E-value: 0
                             TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep..kvkWfedgelnvsyncvdrhvekrkdk 73 
                                           + e+y ++yee++e+p+kfw+k++k +++w+kp++kv+++s++   ++kWfedg++nvsync+drh++++ d+
  NCBI__GCF_000023185.1:WP_012759526.1  19 DKEKYLKWYEESVENPDKFWGKHGK-RIDWFKPYTKVKNTSFTGkvSIKWFEDGQTNVSYNCIDRHLKTNGDQ 90 
                                           6789*********************.5**************9887799************************* PP

                             TIGR02188  74 vaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfa 146
                                           vaiiwegd++    +k+tY+el+++vcr+anvlk++Gvkkgdrv+iY+pmipea++amlacaRiGavhsvvf+
  NCBI__GCF_000023185.1:WP_012759526.1  91 VAIIWEGDNPYI-DKKVTYNELYEHVCRMANVLKKHGVKKGDRVTIYMPMIPEAAYAMLACARIGAVHSVVFG 162
                                           ********9996.99********************************************************** PP

                             TIGR02188 147 GfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee...svekvlvvkrtgeevaewkegrD 216
                                           Gfs+eala Rivd+e+ +vit deglRggk ++lk+++d a++ a +    vekvlvv+rtg + + w  grD
  NCBI__GCF_000023185.1:WP_012759526.1 163 GFSPEALAGRIVDCESTFVITCDEGLRGGKPVPLKNNTDTAIDIAARqhvIVEKVLVVRRTGGK-TGWAPGRD 234
                                           *****************************************98765545689************.56****** PP

                             TIGR02188 217 vwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaD 289
                                           +w ++++++ ++aec+p k+++edplfiLYtsGstGkPkGvlhttgGyl++aa+t++yvfd++++d++wCtaD
  NCBI__GCF_000023185.1:WP_012759526.1 235 LWHHQEIAT-VKAECPPVKMKAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAAMTHEYVFDYHHGDVYWCTAD 306
                                           ********6.*************************************************************** PP

                             TIGR02188 290 vGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlss 362
                                           vGWvtGhsYi+ygPLan attl+fegvp++pd++rfwevi+k+kv+ifYtaPtaiR+lm +g+++v++ ++ss
  NCBI__GCF_000023185.1:WP_012759526.1 307 VGWVTGHSYILYGPLANCATTLMFEGVPNFPDQGRFWEVIDKHKVNIFYTAPTAIRSLMGAGDDFVTRSSRSS 379
                                           ************************************************************************* PP

                             TIGR02188 363 lrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvde 435
                                           lr+lg+vGepinpeaweWyy+vvG+++cp++dtwWqtetGg++itplpg at+lkpgsat+P+fG+++++vd+
  NCBI__GCF_000023185.1:WP_012759526.1 380 LRLLGTVGEPINPEAWEWYYNVVGDKRCPVIDTWWQTETGGHMITPLPG-ATDLKPGSATTPFFGVKPQLVDN 451
                                           *************************************************.6********************** PP

                             TIGR02188 436 egkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvs 508
                                           egk +e  ++ g L+i+++wP+++rt+ygd+erf++tYf+++kg yftGDg+rrd+dGy+wi+GRvDdv+nvs
  NCBI__GCF_000023185.1:WP_012759526.1 452 EGKVLEGPAD-GNLCITDSWPGQMRTVYGDHERFIQTYFSTYKGKYFTGDGCRRDADGYYWITGRVDDVLNVS 523
                                           ******7676.78************************************************************ PP

                             TIGR02188 509 Ghrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdk 581
                                           Ghrlgtae+esalvsh+ v+eaavvg+p+ ikg+ i+++v+l++g+e ++ +l++el k+vr eigpia+pdk
  NCBI__GCF_000023185.1:WP_012759526.1 524 GHRLGTAEVESALVSHNLVSEAAVVGYPHPIKGQGIYCYVTLMAGHEGSD-TLRQELVKHVRGEIGPIAAPDK 595
                                           ***********************************************999.5********************* PP

                             TIGR02188 582 ilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                           i++++ lPktRsGkimRR+lrkiae++  +lgd+stl+dp+vv++l++
  NCBI__GCF_000023185.1:WP_012759526.1 596 IQFAPGLPKTRSGKIMRRILRKIAEDDfGALGDTSTLADPAVVDDLIA 643
                                           ********************************************9975 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 17.12
//
[ok]

This GapMind analysis is from Apr 09 2024. 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