Alignments for a candidate for acs in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Burkholderia phytofirmans PsJN

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate BPHYT_RS27780 BPHYT_RS27780 acetyl-CoA synthetase

Query= SwissProt::P31638
         (660 letters)



>FitnessBrowser__BFirm:BPHYT_RS27780
          Length = 658

 Score = 1028 bits (2657), Expect = 0.0
 Identities = 477/631 (75%), Positives = 555/631 (87%)

Query: 25  AIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTKVLDQSNAPFYKWFEDGELNAS 84
           AI  M+AY+AL  EAE D++ FWAR ARE L W +PFTK+LD SNAPFYKWFEDGELNAS
Sbjct: 23  AISGMDAYRALVAEAETDHQAFWARLAREHLQWRRPFTKILDDSNAPFYKWFEDGELNAS 82

Query: 85  YNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKVCRFANGLKALGIRKGDRVVIY 144
           YNCLDRNL  G ADK AIVFEADDG+VTR+TY+ L+ +VCR AN L+A G+ +GDRVVIY
Sbjct: 83  YNCLDRNLAKGLADKTAIVFEADDGTVTRITYQALYHRVCRLANALRARGVTRGDRVVIY 142

Query: 145 MPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVDVGAVALITADEQMRGGKALPL 204
           MPMS+EG+ AM ACAR+GA HSVVFGGFSAKSL ERLV+VGAVA++TADEQ+RGGK LPL
Sbjct: 143 MPMSIEGIAAMLACARIGAPHSVVFGGFSAKSLHERLVNVGAVAVMTADEQVRGGKTLPL 202

Query: 205 KAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDRWMEDVSAGQPDTCEAEPVSAEHP 264
           KAI D+ALA+GG  AV+ V+VYRRTGG++ W   RD W+ ++   Q DTCE E V AEHP
Sbjct: 203 KAIVDEALAMGGTVAVKTVVVYRRTGGRIPWITQRDAWLHELEHAQSDTCEPEWVGAEHP 262

Query: 265 LFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIKPDDLFWCTADIGWVTGHTYIAY 324
           LFVLYTSGSTG PKGVQHSTGGYLLWA +TMKWTFDIKPDD+FWCTADIGW+TGHTYI Y
Sbjct: 263 LFVLYTSGSTGAPKGVQHSTGGYLLWAAVTMKWTFDIKPDDVFWCTADIGWITGHTYICY 322

Query: 325 GPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTAPTAIRSLIKAAEADEKIHPKQ 384
           GP A GATQV+FEGVPTYP+AGRFW MI RHKVSIFYTAPTAIRSLIKAA+A+E +HP+ 
Sbjct: 323 GPTAVGATQVIFEGVPTYPDAGRFWQMIERHKVSIFYTAPTAIRSLIKAADANEAVHPRS 382

Query: 385 YDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDTFWQTETGGHMITPLPGATPLVP 444
           +DLSSLR+LGTVGEPINP AW WY +++G  RCP++DTFWQTETGGHMI+PLPG TPLVP
Sbjct: 383 FDLSSLRILGTVGEPINPSAWTWYAQHVGGGRCPVLDTFWQTETGGHMISPLPGVTPLVP 442

Query: 445 GSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWPAMIRTIWGDPERFRKSYFPEELG 504
           GSCTLP+PGI AAIVDETGH+VPNG+GG+LV+++PWP+MIRTIWG+PERFR  Y+P++LG
Sbjct: 443 GSCTLPMPGIDAAIVDETGHEVPNGHGGVLVIRKPWPSMIRTIWGNPERFRHGYYPDDLG 502

Query: 505 GKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRMGTMEIESALVSNPLVAEAAVVGRP 564
           GKLYLAGDG+IRD+DTGYFTI GRIDDVLNVSGHR+GTMEIESAL ++P VAEAAVVGRP
Sbjct: 503 GKLYLAGDGAIRDRDTGYFTITGRIDDVLNVSGHRLGTMEIESALSAHPSVAEAAVVGRP 562

Query: 565 DDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVGKEIGPIAKPKDIRFGDNLPKTRSG 624
           D+  GEAI AFVVLK +RP+G +A ++A ELR WVGKEIGPIAKPKDIRFGD +PKTRSG
Sbjct: 563 DETCGEAIVAFVVLKTARPSGPDAKRVADELRAWVGKEIGPIAKPKDIRFGDAMPKTRSG 622

Query: 625 KIMRRLLRSLAKGEEITQDTSTLENPAILEQ 655
           K++RRLLRS+AKGE ITQDTS++ENP ++ Q
Sbjct: 623 KVVRRLLRSVAKGEAITQDTSSVENPTVISQ 653


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: 1574
Number of extensions: 77
Number of successful extensions: 2
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: 658
Length adjustment: 38
Effective length of query: 622
Effective length of database: 620
Effective search space:   385640
Effective search space used:   385640
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 BPHYT_RS27780 BPHYT_RS27780 (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.24901.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   8.3e-288  941.7   0.0   9.5e-288  941.6   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS27780  BPHYT_RS27780 acetyl-CoA synthet


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS27780  BPHYT_RS27780 acetyl-CoA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  941.6   0.0  9.5e-288  9.5e-288       2     626 ..      25     654 ..      24     657 .. 0.97

  Alignments for each domain:
  == domain 1  score: 941.6 bits;  conditional E-value: 9.5e-288
                                TIGR02188   2 aeleeykelyeeaiedpekfwaklakeelewlkpfekvldeslepkvkWfedgelnvsyncvdrhvek.r 70 
                                              + +++y++l++ea++d+++fwa+la+e+l+w +pf+k+ld+s++p++kWfedgeln+sync+dr+++k  
  lcl|FitnessBrowser__BFirm:BPHYT_RS27780  25 SGMDAYRALVAEAETDHQAFWARLAREHLQWRRPFTKILDDSNAPFYKWFEDGELNASYNCLDRNLAKgL 94 
                                              5789****************************************************************99 PP

                                TIGR02188  71 kdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGav 140
                                              +dk+ai++e+d+ +  + ++tY+ l+++vcrlan+l++ Gv +gdrv+iY+pm +e ++amlacaRiGa 
  lcl|FitnessBrowser__BFirm:BPHYT_RS27780  95 ADKTAIVFEADDGT--VTRITYQALYHRVCRLANALRARGVTRGDRVVIYMPMSIEGIAAMLACARIGAP 162
                                              ***********664..89**************************************************** PP

                                TIGR02188 141 hsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeeva 209
                                              hsvvf+Gfsa++l+eR+v++ a  v+tade++Rggk+++lk+ivdeal++  + +v++v+v++rtg  + 
  lcl|FitnessBrowser__BFirm:BPHYT_RS27780 163 HSVVFGGFSAKSLHERLVNVGAVAVMTADEQVRGGKTLPLKAIVDEALAMGGTvAVKTVVVYRRTGGRIP 232
                                              **************************************************9999**************66 PP

                                TIGR02188 210 ewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdik 279
                                               w  +rD w++el +  +s++cepe++++e+plf+LYtsGstG PkGv+h+tgGyll+aa+t+k++fdik
  lcl|FitnessBrowser__BFirm:BPHYT_RS27780 233 -WITQRDAWLHELEHA-QSDTCEPEWVGAEHPLFVLYTSGSTGAPKGVQHSTGGYLLWAAVTMKWTFDIK 300
                                              .************995.***************************************************** PP

                                TIGR02188 280 dedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmk 349
                                              ++d+fwCtaD+GW+tGh+Yi+ygP a+Gat+++fegvptypda+rfw++ie++kv+ifYtaPtaiR+l+k
  lcl|FitnessBrowser__BFirm:BPHYT_RS27780 301 PDDVFWCTADIGWITGHTYICYGPTAVGATQVIFEGVPTYPDAGRFWQMIERHKVSIFYTAPTAIRSLIK 370
                                              ********************************************************************** PP

                                TIGR02188 350 lgee....lvkkhdlsslrvlgsvGepinpeaweWyyevvGkekcpivdtwWqtetGgilitplpgvate 415
                                              ++++    ++++ dlsslr+lg+vGepinp+aw+Wy ++vG ++cp+ dt+WqtetGg++i+plpg +t+
  lcl|FitnessBrowser__BFirm:BPHYT_RS27780 371 AADAneavHPRSFDLSSLRILGTVGEPINPSAWTWYAQHVGGGRCPVLDTFWQTETGGHMISPLPG-VTP 439
                                              9965223357899*****************************************************.5** PP

                                TIGR02188 416 lkpgsatlPlfGieaevvdeegkeveeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkg..lyft 483
                                              l pgs+tlP++Gi+a++vde+g+ev ++++ gvLvi+kpwPsm+rti+g++erf + Y+ +  g  ly++
  lcl|FitnessBrowser__BFirm:BPHYT_RS27780 440 LVPGSCTLPMPGIDAAIVDETGHEVPNGHG-GVLVIRKPWPSMIRTIWGNPERFRHGYYPDDLGgkLYLA 508
                                              ***************************999.8**************************98765557**** PP

                                TIGR02188 484 GDgarrdkd.GyiwilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlke 552
                                              GDga rd+d Gy++i+GR+Ddv+nvsGhrlgt+eiesal +h++vaeaavvg+pde+ geaivafvvlk+
  lcl|FitnessBrowser__BFirm:BPHYT_RS27780 509 GDGAIRDRDtGYFTITGRIDDVLNVSGHRLGTMEIESALSAHPSVAEAAVVGRPDETCGEAIVAFVVLKT 578
                                              *******999***********************************************************9 PP

                                TIGR02188 553 gve..edeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaegeellgdvstledp 620
                                              ++   +d++++++el+++v keigpiakp++i++ +++PktRsGk++RRllr++a+ge +++d+s +e+p
  lcl|FitnessBrowser__BFirm:BPHYT_RS27780 579 ARPsgPDAKRVADELRAWVGKEIGPIAKPKDIRFGDAMPKTRSGKVVRRLLRSVAKGEAITQDTSSVENP 648
                                              9873356669************************************************************ PP

                                TIGR02188 621 svveel 626
                                              +v+ + 
  lcl|FitnessBrowser__BFirm:BPHYT_RS27780 649 TVISQF 654
                                              **9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (658 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: 10.99
//
[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