GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Pseudomonas fluorescens FW300-N2C3

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate AO356_18695 AO356_18695 acetyl-CoA synthetase

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_18695
          Length = 651

 Score = 1332 bits (3448), Expect = 0.0
 Identities = 651/651 (100%), Positives = 651/651 (100%)

Query: 1   MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60
           MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF
Sbjct: 1   MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60

Query: 61  DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKF 120
           DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKF
Sbjct: 61  DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKF 120

Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180
           ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS
Sbjct: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180

Query: 181 KVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDL 240
           KVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDL
Sbjct: 181 KVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDL 240

Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEV 300
           MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEV
Sbjct: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEV 300

Query: 301 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTA 360
           YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTA
Sbjct: 301 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTA 360

Query: 361 IRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGG 420
           IRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGG
Sbjct: 361 IRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGG 420

Query: 421 VLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGD 480
           VLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGD
Sbjct: 421 VLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGD 480

Query: 481 HDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540
           HDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP
Sbjct: 481 HDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540

Query: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAP 600
           KVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAP
Sbjct: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAP 600

Query: 601 GLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIETHKTMNVA 651
           GLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIETHKTMNVA
Sbjct: 601 GLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIETHKTMNVA 651


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: 1737
Number of extensions: 47
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 AO356_18695 AO356_18695 (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.20835.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 1021.5   0.2          0 1021.2   0.2    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695  AO356_18695 acetyl-CoA synthetas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695  AO356_18695 acetyl-CoA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1021.2   0.2         0         0       3     628 ..      20     643 ..      18     644 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1021.2 bits;  conditional E-value: 0
                                       TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsync 62 
                                                     +  +yk++y++++ +p+ fw+++ak+ l+w+kpf++v+++s+++   ++kWf+dg+lnvsync
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695  20 DEATYKAMYQQSVVNPDGFWREQAKR-LDWIKPFTTVKQTSFDDhhvDIKWFADGTLNVSYNC 81 
                                                     5679*********************5.*************99887789*************** PP

                                       TIGR02188  63 vdrhvekrkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmip 125
                                                     +drh+++r d++aiiwegd+++e sr++tY+el++evc++an+l+ + v++gd v+iY+pmip
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695  82 LDRHLAERGDQIAIIWEGDDPSE-SRNITYRELHEEVCKFANALRGQDVHRGDVVTIYMPMIP 143
                                                     *********************96.*************************************** PP

                                       TIGR02188 126 eaviamlacaRiGavhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdeal 188
                                                     eav+amlac+RiGa+hsvvf+Gfs+eala Ri+d+++k+vitadeg+R gk+i+lk++vd+al
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695 144 EAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVITADEGVRAGKKIPLKANVDDAL 206
                                                     *************************************************************** PP

                                       TIGR02188 189 ekaee.svekvlvvkrtgeevaewkegrDvwweelvekeasaecepekldsedplfiLYtsGs 250
                                                     ++ e+ s++kv+v+krt  +++ w++ rD+w+e+l++  a + c+p+++++e+ lfiLYtsGs
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695 207 TNPETsSIQKVIVCKRTAGNIK-WNQHRDIWYEDLMKV-AGTVCAPKEMGAEEALFILYTSGS 267
                                                     **9998**************76.**************5.************************ PP

                                       TIGR02188 251 tGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanGattllf 313
                                                     tGkPkGv+htt+Gyll+aalt++ vfd+k+++++wCtaDvGWvtGhsYivygPLanGattllf
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695 268 TGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWCTADVGWVTGHSYIVYGPLANGATTLLF 330
                                                     *************************************************************** PP

                                       TIGR02188 314 egvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpe 376
                                                     egvp+ypd  r+++vi+k+kv+i+YtaPtaiRa+m+ g+++v+  d sslr+lgsvGepinpe
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695 331 EGVPNYPDITRVAKVIDKHKVSILYTAPTAIRAMMASGTAAVEGADGSSLRLLGSVGEPINPE 393
                                                     *************************************************************** PP

                                       TIGR02188 377 aweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegke 439
                                                     aw+Wyy++vGke+cpivdtwWqtetGg+li+plpg at+lkpgsat+P+fG+ +++vd+ g+ 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695 394 AWDWYYKNVGKERCPIVDTWWQTETGGVLISPLPG-ATALKPGSATRPFFGVVPALVDNLGNL 455
                                                     ***********************************.6************************** PP

                                       TIGR02188 440 veeeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvD 502
                                                     +e  +e g Lvi ++wP+++rt+ygd++rfv+tYfk+++g+yftGDgarrd+dGy+wi+GRvD
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695 456 IEGAAE-GNLVILDSWPGQARTLYGDHDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVD 517
                                                     **8777.79****************************************************** PP

                                       TIGR02188 503 dvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekel 565
                                                     dv+nvsGhr+gtaeiesa+v+h++vaeaavvgvp++ikg+ i+++v+l++g+e++e +l+ el
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695 518 DVLNVSGHRMGTAEIESAMVAHPKVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSE-ALRLEL 579
                                                     *****************************************************999.6***** PP

                                       TIGR02188 566 kklvrkeigpiakpdkilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelk 627
                                                     k++vrkeigpia+pd i++++ lPktRsGkimRR+lrkia+ e + lgd+stl+dp vv++l+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695 580 KNWVRKEIGPIASPDVIQWAPGLPKTRSGKIMRRILRKIATAEyDGLGDISTLADPGVVAHLI 642
                                                     *******************************************9****************998 PP

                                       TIGR02188 628 e 628
                                                     e
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_18695 643 E 643
                                                     6 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: 00:00:00.04
# Mc/sec: 10.06
//
[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