Alignments for a candidate for acs in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Sinorhizobium meliloti 1021

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate SMc04093 SMc04093 acetyl-CoA synthetase

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



>FitnessBrowser__Smeli:SMc04093
          Length = 649

 Score =  885 bits (2286), Expect = 0.0
 Identities = 423/638 (66%), Positives = 500/638 (78%), Gaps = 3/638 (0%)

Query: 7   YPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHVD 66
           YPV       TL D ATY   Y++SV +P+ FW E  KR++W +P+T VK TSF+   V 
Sbjct: 6   YPVLEAAKNRTLLDNATYLEWYRESVADPEKFWGEHGKRIEWFEPYTKVKNTSFEGD-VS 64

Query: 67  IKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANALRG 126
           IKWF DG  NVSYNC+DRHL   G++ AIIWEGD+P   + ITY EL+++VC+ AN L+ 
Sbjct: 65  IKWFEDGLTNVSYNCIDRHLKTHGEKTAIIWEGDNPYLDKKITYNELYDKVCRLANVLKE 124

Query: 127 QDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVITA 186
           Q V +GD VTIYMPMIPEA  AMLAC RIGAIHSVVFGGFSPEALAGRI+DC+S  VIT 
Sbjct: 125 QGVKKGDRVTIYMPMIPEAAYAMLACARIGAIHSVVFGGFSPEALAGRIVDCESTFVITC 184

Query: 187 DEGVRAGKKIPLKANVDDAL--TNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKVA 244
           DEGVR GK + LK N D A+     +  ++ KV+V +RT G + W   RD+WY      A
Sbjct: 185 DEGVRGGKPVALKENTDTAIDIAARQHVTVSKVLVVRRTGGKVGWAPGRDLWYHQETAAA 244

Query: 245 GTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWCT 304
              C P++M AE+ LFILYTSGSTGKPKGV HTT GYL+YA++TH+ VFDY+ G++YWCT
Sbjct: 245 EPHCPPEKMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYASMTHQYVFDYQDGDIYWCT 304

Query: 305 ADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRAM 364
           ADVGWVTGHSYIVYGPLAN ATTL+FEGVPN+PD  R  +V+DKHKV+I YTAPTAIR++
Sbjct: 305 ADVGWVTGHSYIVYGPLANAATTLMFEGVPNFPDAGRFWEVVDKHKVNIFYTAPTAIRSL 364

Query: 365 MASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLIS 424
           M +G   V+ +  SSLRLLG+VGEPINPEAW+WYY  VG ERCP+VDTWWQTETGG+LI+
Sbjct: 365 MGAGDDFVKRSSRSSLRLLGTVGEPINPEAWEWYYHVVGDERCPVVDTWWQTETGGILIT 424

Query: 425 PLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDRF 484
           PLPGAT LKPGSATRPFFGV P +VD+ G +++GAA+GNL I DSWPGQ RT+YGDH+RF
Sbjct: 425 PLPGATDLKPGSATRPFFGVQPQIVDSDGKVVDGAADGNLCITDSWPGQMRTVYGDHERF 484

Query: 485 VDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAE 544
           + TYF T+ G YFTGDG RRDEDGYYWITGRVDDVLNVSGHR+GTAE+ESA+V+H  V+E
Sbjct: 485 IQTYFSTYKGKYFTGDGCRRDEDGYYWITGRVDDVLNVSGHRLGTAEVESALVSHNLVSE 544

Query: 545 AAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLPK 604
           AAVVG PH IKGQGIY YV+L AGE   + LR  L   VR EIGPIA+PD IQ+APGLPK
Sbjct: 545 AAVVGYPHPIKGQGIYCYVSLMAGEVGDDELRQALVKHVRSEIGPIATPDKIQFAPGLPK 604

Query: 605 TRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLI 642
           TRSGKIMRRILRKIA  ++  LGD STLADPGVV  LI
Sbjct: 605 TRSGKIMRRILRKIAEDDFGSLGDTSTLADPGVVDDLI 642


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: 1468
Number of extensions: 72
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: 651
Length of database: 649
Length adjustment: 38
Effective length of query: 613
Effective length of database: 611
Effective search space:   374543
Effective search space used:   374543
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 SMc04093 SMc04093 (acetyl-CoA synthetase)
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.26859.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 1034.6   0.0          0 1034.4   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMc04093  SMc04093 acetyl-CoA synthetase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc04093  SMc04093 acetyl-CoA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1034.4   0.0         0         0       4     628 ..      20     643 ..      17     644 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1034.4 bits;  conditional E-value: 0
                           TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep..kvkWfedgelnvsyncvdrhvekrkdkvai 76 
                                         + +y e+y+e+++dpekfw++++k ++ew++p++kv+++s+e   ++kWfedg +nvsync+drh++++ +k+ai
  lcl|FitnessBrowser__Smeli:SMc04093  20 NATYLEWYRESVADPEKFWGEHGK-RIEWFEPYTKVKNTSFEGdvSIKWFEDGLTNVSYNCIDRHLKTHGEKTAI 93 
                                         57899*******************.5***************987899**************************** PP

                           TIGR02188  77 iwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsae 151
                                         iwegd++    +k+tY+el+++vcrlanvlke+Gvkkgdrv+iY+pmipea++amlacaRiGa+hsvvf+Gfs+e
  lcl|FitnessBrowser__Smeli:SMc04093  94 IWEGDNPYL-DKKITYNELYDKVCRLANVLKEQGVKKGDRVTIYMPMIPEAAYAMLACARIGAIHSVVFGGFSPE 167
                                         *****9996.9**************************************************************** PP

                           TIGR02188 152 alaeRivdaeaklvitadeglRggkvielkkivdealekaee...svekvlvvkrtgeevaewkegrDvwweelv 223
                                         ala Rivd+e+ +vit deg+Rggk ++lk+++d a++ a +   +v+kvlvv+rtg +v  w  grD+w+++++
  lcl|FitnessBrowser__Smeli:SMc04093 168 ALAGRIVDCESTFVITCDEGVRGGKPVALKENTDTAIDIAARqhvTVSKVLVVRRTGGKVG-WAPGRDLWYHQET 241
                                         ************************************9876554579*************76.************* PP

                           TIGR02188 224 ekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsY 298
                                         +  a+ +c+pek+++edplfiLYtsGstGkPkGvlhttgGyl++a++t++yvfd++d+di+wCtaDvGWvtGhsY
  lcl|FitnessBrowser__Smeli:SMc04093 242 AA-AEPHCPPEKMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYASMTHQYVFDYQDGDIYWCTADVGWVTGHSY 315
                                         *5.************************************************************************ PP

                           TIGR02188 299 ivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepi 373
                                         ivygPLan attl+fegvp++pda+rfwev++k+kv+ifYtaPtaiR+lm +g+++vk+ ++sslr+lg+vGepi
  lcl|FitnessBrowser__Smeli:SMc04093 316 IVYGPLANAATTLMFEGVPNFPDAGRFWEVVDKHKVNIFYTAPTAIRSLMGAGDDFVKRSSRSSLRLLGTVGEPI 390
                                         *************************************************************************** PP

                           TIGR02188 374 npeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggv 448
                                         npeaweWyy+vvG+e+cp+vdtwWqtetGgilitplpg at+lkpgsat+P+fG+++++vd++gk v+  ++ g 
  lcl|FitnessBrowser__Smeli:SMc04093 391 NPEAWEWYYHVVGDERCPVVDTWWQTETGGILITPLPG-ATDLKPGSATRPFFGVQPQIVDSDGKVVDGAAD-GN 463
                                         **************************************.6***************************98777.79 PP

                           TIGR02188 449 LvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvs 523
                                         L+i+++wP+++rt+ygd+erf++tYf+++kg yftGDg+rrd+dGy+wi+GRvDdv+nvsGhrlgtae+esalvs
  lcl|FitnessBrowser__Smeli:SMc04093 464 LCITDSWPGQMRTVYGDHERFIQTYFSTYKGKYFTGDGCRRDEDGYYWITGRVDDVLNVSGHRLGTAEVESALVS 538
                                         *************************************************************************** PP

                           TIGR02188 524 heavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimR 598
                                         h+ v+eaavvg+p+ ikg+ i+++v l++g+  d+ el++ l k+vr+eigpia+pdki++++ lPktRsGkimR
  lcl|FitnessBrowser__Smeli:SMc04093 539 HNLVSEAAVVGYPHPIKGQGIYCYVSLMAGEVGDD-ELRQALVKHVRSEIGPIATPDKIQFAPGLPKTRSGKIMR 612
                                         *****************************999999.5************************************** PP

                           TIGR02188 599 Rllrkiaege.ellgdvstledpsvveelke 628
                                         R+lrkiae++  +lgd+stl+dp vv++l++
  lcl|FitnessBrowser__Smeli:SMc04093 613 RILRKIAEDDfGSLGDTSTLADPGVVDDLIA 643
                                         ***************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (649 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: 0.03u 0.02s 00:00:00.05 Elapsed: 00:00:00.05
# Mc/sec: 8.11
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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