Alignments for a candidate for acs in Synechococcus elongatus PCC 7942

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Synechococcus elongatus PCC 7942

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate Synpcc7942_1352 Synpcc7942_1352 acetyl-CoA synthetase

Query= SwissProt::P31638
         (660 letters)



>FitnessBrowser__SynE:Synpcc7942_1352
          Length = 656

 Score =  758 bits (1956), Expect = 0.0
 Identities = 376/658 (57%), Positives = 480/658 (72%), Gaps = 12/658 (1%)

Query: 4   IESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTK 63
           IES++QE RVF P   FAS A I + EAY+ALC +A  D   FW   A + L W +P+ +
Sbjct: 6   IESILQEKRVFPPSAEFASAARI-NPEAYEALCQKAAADPVAFWGELAAQELDWFEPWQQ 64

Query: 64  VLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKV 123
            LD SN PF KWF  G+LN S+NCLDR+L     +K AI++E + G    +TY +LH +V
Sbjct: 65  TLDWSNPPFAKWFVGGKLNISHNCLDRHLTTWRKNKAAIIWEGEPGDSRTLTYAQLHREV 124

Query: 124 CRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVD 183
           C+FAN LK+LGI+KGD V +YMPM  E  +AM ACAR+GA HSVVFGGFSA++L++RLVD
Sbjct: 125 CQFANVLKSLGIQKGDVVGVYMPMIPEAAIAMLACARIGAVHSVVFGGFSAEALRDRLVD 184

Query: 184 VGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDRWM 243
             A  ++TAD   R    +PLK   D AL    C +V++V+V  RT   +    GRD W 
Sbjct: 185 GQAKLVVTADGGWRKDAIVPLKDSVDQALEGNACPSVQHVLVVERTKQDIHMEPGRDHWW 244

Query: 244 EDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIKP 303
            ++      TC AEP+ +E  LFVLYTSGSTGKPKGV H+TGGY L+A +T +WTFD++ 
Sbjct: 245 HELQQTVSATCPAEPMDSEDLLFVLYTSGSTGKPKGVVHTTGGYNLYAHITTQWTFDLQD 304

Query: 304 DDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTA 363
            D++WCTAD+GW+TGH+YI YGPL+ GAT +++EG P   N G FWD+I ++ V+ FYTA
Sbjct: 305 TDVYWCTADVGWITGHSYIVYGPLSNGATTLMYEGAPRASNPGCFWDVIEKYGVTTFYTA 364

Query: 364 PTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDTF 423
           PTAIR+ IK  E     HP   DLSSLRLLGTVGEPINPEAW+WY++ IG +RCPIVDT+
Sbjct: 365 PTAIRAFIKMGEQ----HPAARDLSSLRLLGTVGEPINPEAWIWYHRVIGGDRCPIVDTW 420

Query: 424 WQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWPAM 483
           WQTETGGHMIT LPGA P  PGS T P PGI+A +VD  G  VP+  GG LV++ PWP M
Sbjct: 421 WQTETGGHMITSLPGAVPTKPGSATKPFPGILADVVDLDGRSVPDNEGGYLVIRHPWPGM 480

Query: 484 IRTIWGDPERFRKSYF---PEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRM 540
           +RT++GDP+RFR++Y+   P + G  LY AGDG+ RD D GYF +MGR+DDV+NVSGHR+
Sbjct: 481 MRTVYGDPDRFRRTYWEHIPPQNGQYLYFAGDGARRDAD-GYFWVMGRVDDVINVSGHRL 539

Query: 541 GTMEIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVG 600
           GTMEIESALVS+P VAEAAVVGRPDD+ GE I AF+ L+    TG+E VK   +L+  V 
Sbjct: 540 GTMEIESALVSHPAVAEAAVVGRPDDLKGEGIVAFITLESGIETGDELVK---DLKKHVA 596

Query: 601 KEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLKQ 658
           +EIG IA+P +IRF + LPKTRSGKIMRRLLRSLA G+E++ DTSTLE+ ++L++L+Q
Sbjct: 597 QEIGAIARPDEIRFSEALPKTRSGKIMRRLLRSLAAGQEVSGDTSTLEDRSVLDKLRQ 654


Lambda     K      H
   0.319    0.136    0.422 

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: 1408
Number of extensions: 67
Number of successful extensions: 6
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: 660
Length of database: 656
Length adjustment: 38
Effective length of query: 622
Effective length of database: 618
Effective search space:   384396
Effective search space used:   384396
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate Synpcc7942_1352 Synpcc7942_1352 (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.29180.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 1022.8   0.0          0 1022.5   0.0    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_1352  Synpcc7942_1352 acetyl-CoA synth


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_1352  Synpcc7942_1352 acetyl-CoA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1022.5   0.0         0         0       3     628 ..      29     654 ..      27     655 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1022.5 bits;  conditional E-value: 0
                                 TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.r 70 
                                               + e+y++l+++a++dp +fw++la +el+w++p++++ld+s++p++kWf++g+ln+s nc+drh+++ r
  lcl|FitnessBrowser__SynE:Synpcc7942_1352  29 NPEAYEALCQKAAADPVAFWGELAAQELDWFEPWQQTLDWSNPPFAKWFVGGKLNISHNCLDRHLTTwR 97 
                                               6789***************************************************************** PP

                                 TIGR02188  71 kdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGa 139
                                               k+k+aiiweg+ +g dsr+ltYa+l+revc++anvlk+lG++kgd v +Y+pmipea+iamlacaRiGa
  lcl|FitnessBrowser__SynE:Synpcc7942_1352  98 KNKAAIIWEGE-PG-DSRTLTYAQLHREVCQFANVLKSLGIQKGDVVGVYMPMIPEAAIAMLACARIGA 164
                                               ***********.77.59**************************************************** PP

                                 TIGR02188 140 vhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgee 207
                                               vhsvvf+Gfsaeal++R+vd +aklv+tad+g+R++ +++lk+ vd+ale   + sv++vlvv+rt+++
  lcl|FitnessBrowser__SynE:Synpcc7942_1352 165 VHSVVFGGFSAEALRDRLVDGQAKLVVTADGGWRKDAIVPLKDSVDQALEGNACpSVQHVLVVERTKQD 233
                                               **************************************************99888************** PP

                                 TIGR02188 208 vaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvf 276
                                               ++ ++ grD+ww+el ++ +sa+c++e++dsed+lf+LYtsGstGkPkGv+httgGy l+a++t++++f
  lcl|FitnessBrowser__SynE:Synpcc7942_1352 234 IH-MEPGRDHWWHELQQT-VSATCPAEPMDSEDLLFVLYTSGSTGKPKGVVHTTGGYNLYAHITTQWTF 300
                                               76.**************6.************************************************** PP

                                 TIGR02188 277 dikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiR 345
                                               d++d+d++wCtaDvGW+tGhsYivygPL+nGattl++eg+p+ +++++fw+vieky+vt+fYtaPtaiR
  lcl|FitnessBrowser__SynE:Synpcc7942_1352 301 DLQDTDVYWCTADVGWITGHSYIVYGPLSNGATTLMYEGAPRASNPGCFWDVIEKYGVTTFYTAPTAIR 369
                                               ********************************************************************* PP

                                 TIGR02188 346 almklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvat 414
                                               a++k+ge++++++dlsslr+lg+vGepinpeaw Wy++v+G ++cpivdtwWqtetGg++it+lpg a+
  lcl|FitnessBrowser__SynE:Synpcc7942_1352 370 AFIKMGEQHPAARDLSSLRLLGTVGEPINPEAWIWYHRVIGGDRCPIVDTWWQTETGGHMITSLPG-AV 437
                                               ******************************************************************.6* PP

                                 TIGR02188 415 elkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkg.... 479
                                               ++kpgsat+P++Gi a+vvd +g++v ++e+ g+Lvi++pwP+m+rt+ygd++rf +tY+++++     
  lcl|FitnessBrowser__SynE:Synpcc7942_1352 438 PTKPGSATKPFPGILADVVDLDGRSVPDNEG-GYLVIRHPWPGMMRTVYGDPDRFRRTYWEHIPPqngq 505
                                               ***************************9999.8*****************************9877888 PP

                                 TIGR02188 480 .lyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivaf 547
                                                lyf+GDgarrd+dGy+w++GRvDdvinvsGhrlgt+eiesalvsh+avaeaavvg+pd++kge ivaf
  lcl|FitnessBrowser__SynE:Synpcc7942_1352 506 yLYFAGDGARRDADGYFWVMGRVDDVINVSGHRLGTMEIESALVSHPAVAEAAVVGRPDDLKGEGIVAF 574
                                               89******************************************************************* PP

                                 TIGR02188 548 vvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaegeellgdvst 616
                                               ++l++g+e+ +e l k+lkk+v++eig+ia+pd+i++ e+lPktRsGkimRRllr++a+g+e+ gd+st
  lcl|FitnessBrowser__SynE:Synpcc7942_1352 575 ITLESGIETGDE-LVKDLKKHVAQEIGAIARPDEIRFSEALPKTRSGKIMRRLLRSLAAGQEVSGDTST 642
                                               **********95.******************************************************** PP

                                 TIGR02188 617 ledpsvveelke 628
                                               led+sv+++l++
  lcl|FitnessBrowser__SynE:Synpcc7942_1352 643 LEDRSVLDKLRQ 654
                                               ********9986 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 11.80
//
[ok]

This GapMind analysis is from Sep 17 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, or view the source code.

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