GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Pseudomonas stutzeri RCH2

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate GFF2607 Psest_2657 acetate--CoA ligase

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



>FitnessBrowser__psRCH2:GFF2607
          Length = 651

 Score = 1132 bits (2927), Expect = 0.0
 Identities = 534/648 (82%), Positives = 588/648 (90%)

Query: 1   MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60
           M AAS+YPV PE A  +LTDEA Y+AMYQQSV+NP+GFWREQA RL+WI+PFT VK+TSF
Sbjct: 1   MCAASVYPVSPEAAKHSLTDEAAYRAMYQQSVINPEGFWREQAARLNWIRPFTEVKRTSF 60

Query: 61  DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKF 120
           DDHHVDIKWFADGTLNVS NCLDRHLAERGDQ+AIIWEGD+PSE R ITYREL++EVCKF
Sbjct: 61  DDHHVDIKWFADGTLNVSANCLDRHLAERGDQVAIIWEGDEPSEHREITYRELYQEVCKF 120

Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180
           ANALRGQDVHRGDVVTIYMPMIPEA VAMLAC RIGAIHSVVFGGFSPEALAGRIID +S
Sbjct: 121 ANALRGQDVHRGDVVTIYMPMIPEAAVAMLACARIGAIHSVVFGGFSPEALAGRIIDGQS 180

Query: 181 KVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDL 240
           KVVITADEG+R GK IPLK NVD+ALT+P+T  +QK+IV +RT  +I+W+ HRD+ Y+DL
Sbjct: 181 KVVITADEGIRGGKPIPLKENVDEALTHPQTRCVQKIIVVRRTGADIRWHPHRDVCYDDL 240

Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEV 300
           M+VAG VCAPKEMGAEE LFILYTSGSTGKPKGV HT  GYLLYAALTHERVFDY+PG+V
Sbjct: 241 MRVAGEVCAPKEMGAEEPLFILYTSGSTGKPKGVLHTCGGYLLYAALTHERVFDYRPGDV 300

Query: 301 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTA 360
           YWCTAD+GW+TGHSY++YGPLANGATTL++EGVPNYPD+TR+A++IDKH+V+ILYTAPTA
Sbjct: 301 YWCTADIGWITGHSYLIYGPLANGATTLMYEGVPNYPDVTRIARIIDKHRVNILYTAPTA 360

Query: 361 IRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGG 420
           IRAMMA G AA+EGADGSSLRLLG+VGEPINPEAW WYY+ VG+ RCPIVDTWWQTETGG
Sbjct: 361 IRAMMAEGAAAMEGADGSSLRLLGTVGEPINPEAWHWYYETVGRSRCPIVDTWWQTETGG 420

Query: 421 VLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGD 480
           +LISPLPGATALKPGSATRP FGVVP LVDNLGNL+EG AEGNLVILDSWPGQ RT+Y D
Sbjct: 421 ILISPLPGATALKPGSATRPLFGVVPGLVDNLGNLLEGPAEGNLVILDSWPGQMRTIYRD 480

Query: 481 HDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540
           HDRFVDTYFKTF GMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAH 
Sbjct: 481 HDRFVDTYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHA 540

Query: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAP 600
           KVAEAA VGVPH +KGQ IYVYVTL AG E S+ LR EL+ WVR EIGPIA PD IQWAP
Sbjct: 541 KVAEAAAVGVPHALKGQAIYVYVTLVAGVEPSDTLRQELQQWVRHEIGPIAVPDTIQWAP 600

Query: 601 GLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIETHKTM 648
           GLPKTRSGKIMRR+LRKIAT +YD LGD STLADPGVV  LIE H+ +
Sbjct: 601 GLPKTRSGKIMRRLLRKIATDDYDALGDTSTLADPGVVDQLIEAHEAV 648


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: 1625
Number of extensions: 60
Number of successful extensions: 1
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: 651
Length adjustment: 38
Effective length of query: 613
Effective length of database: 613
Effective search space:   375769
Effective search space used:   375769
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 GFF2607 Psest_2657 (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.15946.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-307 1005.5   0.0   4.8e-307 1005.3   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF2607  Psest_2657 acetate--CoA ligase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF2607  Psest_2657 acetate--CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1005.3   0.0  4.8e-307  4.8e-307       4     628 ..      21     643 ..      18     644 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1005.3 bits;  conditional E-value: 4.8e-307
                           TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdkva 75 
                                           +y+++y++++ +pe fw+++a  +l+w++pf++v+++s+++   ++kWf+dg+lnvs+nc+drh+++r d+va
  lcl|FitnessBrowser__psRCH2:GFF2607  21 EAAYRAMYQQSVINPEGFWREQAA-RLNWIRPFTEVKRTSFDDhhvDIKWFADGTLNVSANCLDRHLAERGDQVA 94 
                                         678*********************.5*************99887789**************************** PP

                           TIGR02188  76 iiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsa 150
                                         iiwegde++e +r++tY+el++evc++an+l+ + v++gd v+iY+pmipea++amlacaRiGa+hsvvf+Gfs+
  lcl|FitnessBrowser__psRCH2:GFF2607  95 IIWEGDEPSE-HREITYRELYQEVCKFANALRGQDVHRGDVVTIYMPMIPEAAVAMLACARIGAIHSVVFGGFSP 168
                                         ********96.**************************************************************** PP

                           TIGR02188 151 ealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvwweelve 224
                                         eala Ri+d ++k+vitadeg+Rggk i+lk++vdeal++ ++  v+k++vv+rtg+++  w+  rDv +++l++
  lcl|FitnessBrowser__psRCH2:GFF2607 169 EALAGRIIDGQSKVVITADEGIRGGKPIPLKENVDEALTHPQTrCVQKIIVVRRTGADIR-WHPHRDVCYDDLMR 242
                                         ****************************************99889*************76.************** PP

                           TIGR02188 225 keasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYi 299
                                           a + c+p+++++e+plfiLYtsGstGkPkGvlht gGyll+aalt++ vfd++++d++wCtaD+GW+tGhsY+
  lcl|FitnessBrowser__psRCH2:GFF2607 243 V-AGEVCAPKEMGAEEPLFILYTSGSTGKPKGVLHTCGGYLLYAALTHERVFDYRPGDVYWCTADIGWITGHSYL 316
                                         5.************************************************************************* PP

                           TIGR02188 300 vygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepin 374
                                         +ygPLanGattl++egvp+ypd  r++++i+k++v+i+YtaPtaiRa+m++g ++++  d sslr+lg+vGepin
  lcl|FitnessBrowser__psRCH2:GFF2607 317 IYGPLANGATTLMYEGVPNYPDVTRIARIIDKHRVNILYTAPTAIRAMMAEGAAAMEGADGSSLRLLGTVGEPIN 391
                                         *************************************************************************** PP

                           TIGR02188 375 peaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvL 449
                                         peaw+Wyye+vG+++cpivdtwWqtetGgili+plpg at+lkpgsat+PlfG+ + +vd+ g+ +e  +e g L
  lcl|FitnessBrowser__psRCH2:GFF2607 392 PEAWHWYYETVGRSRCPIVDTWWQTETGGILISPLPG-ATALKPGSATRPLFGVVPGLVDNLGNLLEGPAE-GNL 464
                                         *************************************.6****************************7666.68* PP

                           TIGR02188 450 vikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsh 524
                                         vi ++wP+++rtiy+d++rfv+tYfk+++g+yftGDgarrd+dGy+wi+GRvDdv+nvsGhr+gtaeiesa+v+h
  lcl|FitnessBrowser__psRCH2:GFF2607 465 VILDSWPGQMRTIYRDHDRFVDTYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAH 539
                                         *************************************************************************** PP

                           TIGR02188 525 eavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRR 599
                                          +vaeaa+vgvp+ +kg+ai+++v+l +gve++++ l++el+++vr+eigpia pd+i++++ lPktRsGkimRR
  lcl|FitnessBrowser__psRCH2:GFF2607 540 AKVAEAAAVGVPHALKGQAIYVYVTLVAGVEPSDT-LRQELQQWVRHEIGPIAVPDTIQWAPGLPKTRSGKIMRR 613
                                         **********************************5.*************************************** PP

                           TIGR02188 600 llrkiaege.ellgdvstledpsvveelke 628
                                         llrkia+++ ++lgd+stl+dp vv++l+e
  lcl|FitnessBrowser__psRCH2:GFF2607 614 LLRKIATDDyDALGDTSTLADPGVVDQLIE 643
                                         *********9*****************987 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 12.41
//
[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:

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:

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:

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:

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