Alignments for a candidate for acs in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Cupriavidus basilensis 4G11

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate RR42_RS13880 RR42_RS13880 AMP-dependent synthetase

Query= SwissProt::P31638
         (660 letters)



>FitnessBrowser__Cup4G11:RR42_RS13880
          Length = 660

 Score = 1286 bits (3327), Expect = 0.0
 Identities = 619/660 (93%), Positives = 645/660 (97%)

Query: 1   MSAIESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKP 60
           MSAIESVMQEHR+FNPPE FA QAAIPSMEAYQALCDEAERDYEGFWARHARE LHWTKP
Sbjct: 1   MSAIESVMQEHRIFNPPESFAKQAAIPSMEAYQALCDEAERDYEGFWARHAREQLHWTKP 60

Query: 61  FTKVLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELH 120
           FTKVLD+SNAPFYKWFEDGELNAS+NCLDRNL NGNA+KVAIVFEADDG+VTRVTYR+LH
Sbjct: 61  FTKVLDESNAPFYKWFEDGELNASFNCLDRNLDNGNAEKVAIVFEADDGTVTRVTYRQLH 120

Query: 121 GKVCRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQER 180
            KVC+FANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQER
Sbjct: 121 AKVCQFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQER 180

Query: 181 LVDVGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRD 240
           LVDVGAVALITADEQMRGGKALPLKAIAD+ALALGGCEAV++VIVYRRTGGKV W EGRD
Sbjct: 181 LVDVGAVALITADEQMRGGKALPLKAIADEALALGGCEAVKSVIVYRRTGGKVNWAEGRD 240

Query: 241 RWMEDVSAGQPDTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFD 300
           RWM+DV+AGQP TCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKW+FD
Sbjct: 241 RWMDDVAAGQPQTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWSFD 300

Query: 301 IKPDDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIF 360
           IKPDD+FWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIF
Sbjct: 301 IKPDDMFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIF 360

Query: 361 YTAPTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIV 420
           YTAPTAIRSLIKAAEADEKIHP+QYDLSSLRLLGTVGEPINPEAWMWYY+NIG ERCP+V
Sbjct: 361 YTAPTAIRSLIKAAEADEKIHPRQYDLSSLRLLGTVGEPINPEAWMWYYQNIGGERCPVV 420

Query: 421 DTFWQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPW 480
           DTFWQTETGGHMITPLPGATPLVPGSCTLPLPGI+AAIVDETG DVPNG+GGILVVKRPW
Sbjct: 421 DTFWQTETGGHMITPLPGATPLVPGSCTLPLPGIIAAIVDETGQDVPNGSGGILVVKRPW 480

Query: 481 PAMIRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRM 540
           P+MIRTIWGDPERF+KSYFPEELGGKLYLAGDGSIRDK+TGYFTIMGRIDDVLNVSGHRM
Sbjct: 481 PSMIRTIWGDPERFKKSYFPEELGGKLYLAGDGSIRDKETGYFTIMGRIDDVLNVSGHRM 540

Query: 541 GTMEIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVG 600
           GTMEIESALVSNP+VAEAAVVGRPDDMTGEAICAFVVLKRSRP  EEA +IA +LRNWVG
Sbjct: 541 GTMEIESALVSNPIVAEAAVVGRPDDMTGEAICAFVVLKRSRPNEEEAKQIAADLRNWVG 600

Query: 601 KEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLKQAQ 660
           KEIGPIAKP+DIRFGDNLPKTRSGKIMRRLLRSLAK EEITQDTSTLENPAILEQLKQAQ
Sbjct: 601 KEIGPIAKPRDIRFGDNLPKTRSGKIMRRLLRSLAKNEEITQDTSTLENPAILEQLKQAQ 660


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: 1661
Number of extensions: 69
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: 660
Length of database: 660
Length adjustment: 38
Effective length of query: 622
Effective length of database: 622
Effective search space:   386884
Effective search space used:   386884
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 RR42_RS13880 RR42_RS13880 (AMP-dependent 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.28893.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.1e-300  982.4   0.0   4.7e-300  982.2   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS13880  RR42_RS13880 AMP-dependent synth


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS13880  RR42_RS13880 AMP-dependent synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  982.2   0.0  4.7e-300  4.7e-300       3     628 ..      28     658 ..      26     659 .. 0.97

  Alignments for each domain:
  == domain 1  score: 982.2 bits;  conditional E-value: 4.7e-300
                                 TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.r 70 
                                               ++e+y++l++ea++d+e fwa++a+e+l+w+kpf+kvldes++p++kWfedgeln+s+nc+dr++ + +
  lcl|FitnessBrowser__Cup4G11:RR42_RS13880  28 SMEAYQALCDEAERDYEGFWARHAREQLHWTKPFTKVLDESNAPFYKWFEDGELNASFNCLDRNLDNgN 96 
                                               6899***************************************************************9* PP

                                 TIGR02188  71 kdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGa 139
                                               ++kvai++e+d+ +  + ++tY++l+++vc++an lk+lG++kgdrv+iY+pm +e v+am+acaR+Ga
  lcl|FitnessBrowser__Cup4G11:RR42_RS13880  97 AEKVAIVFEADDGT--VTRVTYRQLHAKVCQFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGA 163
                                               ***********664..89*************************************************** PP

                                 TIGR02188 140 vhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgee 207
                                               +hsvvf+Gfsa++l+eR+vd+ a  +itade++Rggk+++lk+i+deal+   + +v++v+v++rtg +
  lcl|FitnessBrowser__Cup4G11:RR42_RS13880 164 THSVVFGGFSAKSLQERLVDVGAVALITADEQMRGGKALPLKAIADEALALGGCeAVKSVIVYRRTGGK 232
                                               *************************************************9988779************* PP

                                 TIGR02188 208 vaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvf 276
                                               v+ w egrD w++++ + +++++ce+e++++e+plf+LYtsGstGkPkGv+h+tgGyll+a +t+k+ f
  lcl|FitnessBrowser__Cup4G11:RR42_RS13880 233 VN-WAEGRDRWMDDVAA-GQPQTCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWSF 299
                                               66.**************.6************************************************** PP

                                 TIGR02188 277 dikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiR 345
                                               dik++d+fwCtaD+GWvtGh+Yi ygPLa+Gat+++fegvptyp+a+rfw++i ++kv+ifYtaPtaiR
  lcl|FitnessBrowser__Cup4G11:RR42_RS13880 300 DIKPDDMFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTAPTAIR 368
                                               ********************************************************************* PP

                                 TIGR02188 346 almklgee....lvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplp 410
                                               +l+k++e+    +++++dlsslr+lg+vGepinpeaw+Wyy+++G e+cp+vdt+WqtetGg++itplp
  lcl|FitnessBrowser__Cup4G11:RR42_RS13880 369 SLIKAAEAdekiHPRQYDLSSLRLLGTVGEPINPEAWMWYYQNIGGERCPVVDTFWQTETGGHMITPLP 437
                                               ****985422337899***************************************************** PP

                                 TIGR02188 411 gvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkg 479
                                               g at+l pgs+tlPl+Gi a++vde+g++v ++++ g+Lv+k+pwPsm+rti+gd+erf ++Yf +  g
  lcl|FitnessBrowser__Cup4G11:RR42_RS13880 438 G-ATPLVPGSCTLPLPGIIAAIVDETGQDVPNGSG-GILVVKRPWPSMIRTIWGDPERFKKSYFPEELG 504
                                               *.6*****************************999.8***************************98765 PP

                                 TIGR02188 480 ..lyftGDgarrdkd.GyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaiv 545
                                                 ly++GDg+ rdk+ Gy++i+GR+Ddv+nvsGhr+gt+eiesalvs++ vaeaavvg+pd+++geai+
  lcl|FitnessBrowser__Cup4G11:RR42_RS13880 505 gkLYLAGDGSIRDKEtGYFTIMGRIDDVLNVSGHRMGTMEIESALVSNPIVAEAAVVGRPDDMTGEAIC 573
                                               67***********988***************************************************** PP

                                 TIGR02188 546 afvvlkegveedee..elekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaegeellg 612
                                               afvvlk+++ ++ee  +++++l+++v keigpiakp++i++ ++lPktRsGkimRRllr++a++ee+++
  lcl|FitnessBrowser__Cup4G11:RR42_RS13880 574 AFVVLKRSRPNEEEakQIAADLRNWVGKEIGPIAKPRDIRFGDNLPKTRSGKIMRRLLRSLAKNEEITQ 642
                                               *******9987776669**************************************************** PP

                                 TIGR02188 613 dvstledpsvveelke 628
                                               d+stle+p+++e+lk+
  lcl|FitnessBrowser__Cup4G11:RR42_RS13880 643 DTSTLENPAILEQLKQ 658
                                               *************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (660 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.04
# Mc/sec: 8.31
//
[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
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