GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Pseudomonas fluorescens FW300-N2E2

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate Pf6N2E2_5659 Acetyl-coenzyme A synthetase (EC 6.2.1.1)

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



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5659
          Length = 646

 Score = 1313 bits (3399), Expect = 0.0
 Identities = 637/646 (98%), Positives = 644/646 (99%)

Query: 6   LYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHV 65
           +YPVRPEVAA+TLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHV
Sbjct: 1   VYPVRPEVAANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHV 60

Query: 66  DIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANALR 125
           DIKWFADGTLNVSYNCLDRHLAERGDQ+AIIWEGDDP+ESRNITYRELHEEVCKFANALR
Sbjct: 61  DIKWFADGTLNVSYNCLDRHLAERGDQVAIIWEGDDPAESRNITYRELHEEVCKFANALR 120

Query: 126 GQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVIT 185
           GQDVHRGDVVTIYMPMIPEAVVAMLAC RIGAIHSVVFGGFSPEALAGRIIDCKSKVVIT
Sbjct: 121 GQDVHRGDVVTIYMPMIPEAVVAMLACARIGAIHSVVFGGFSPEALAGRIIDCKSKVVIT 180

Query: 186 ADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKVAG 245
           ADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKVAG
Sbjct: 181 ADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKVAG 240

Query: 246 TVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWCTA 305
           TVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPG+VYWCTA
Sbjct: 241 TVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGDVYWCTA 300

Query: 306 DVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRAMM 365
           DVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKV+DKHKV+ILYTAPTAIRAMM
Sbjct: 301 DVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVVDKHKVNILYTAPTAIRAMM 360

Query: 366 ASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLISP 425
           ASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLISP
Sbjct: 361 ASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLISP 420

Query: 426 LPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDRFV 485
           LPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDRFV
Sbjct: 421 LPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDRFV 480

Query: 486 DTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAEA 545
           DTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAEA
Sbjct: 481 DTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAEA 540

Query: 546 AVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLPKT 605
           AVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLPKT
Sbjct: 541 AVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLPKT 600

Query: 606 RSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIETHKTMNVA 651
           RSGKIMRRILRKIATAEYDGLGDISTLADP VVAHLIETHKTMNVA
Sbjct: 601 RSGKIMRRILRKIATAEYDGLGDISTLADPSVVAHLIETHKTMNVA 646


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: 1717
Number of extensions: 46
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: 646
Length adjustment: 38
Effective length of query: 613
Effective length of database: 608
Effective search space:   372704
Effective search space used:   372704
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 Pf6N2E2_5659 (Acetyl-coenzyme A synthetase (EC 6.2.1.1))
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.6115.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 1025.9   0.2          0 1025.7   0.2    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5659  Acetyl-coenzyme A synthetase (EC


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5659  Acetyl-coenzyme A synthetase (EC 6.2.1.1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1025.7   0.2         0         0       3     628 ..      15     638 ..      13     639 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1025.7 bits;  conditional E-value: 0
                                      TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncv 63 
                                                    +  +yk++y++++ +p+ fw+++ak+ l+w+kpf++v+++s+++   ++kWf+dg+lnvsync+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5659  15 DEATYKAMYQQSVVNPDGFWREQAKR-LDWIKPFTTVKQTSFDDhhvDIKWFADGTLNVSYNCL 77 
                                                    5679*********************5.*************99887789**************** PP

                                      TIGR02188  64 drhvekrkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipea 127
                                                    drh+++r d+vaiiwegd++ e sr++tY+el++evc++an+l+ + v++gd v+iY+pmipea
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5659  78 DRHLAERGDQVAIIWEGDDPAE-SRNITYRELHEEVCKFANALRGQDVHRGDVVTIYMPMIPEA 140
                                                    ********************96.***************************************** PP

                                      TIGR02188 128 viamlacaRiGavhsvvfaGfsaealaeRivdaeaklvitadeglRggkvielkkivdealeka 191
                                                    v+amlacaRiGa+hsvvf+Gfs+eala Ri+d+++k+vitadeg+R gk+i+lk++vd+al++ 
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5659 141 VVAMLACARIGAIHSVVFGGFSPEALAGRIIDCKSKVVITADEGVRAGKKIPLKANVDDALTNP 204
                                                    ***************************************************************9 PP

                                      TIGR02188 192 ee.svekvlvvkrtgeevaewkegrDvwweelvekeasaecepekldsedplfiLYtsGstGkP 254
                                                    e+ s++kv+v+krt  +++ w++ rD+w+e+l++  a + c+p+++++e+ lfiLYtsGstGkP
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5659 205 ETsSIQKVIVCKRTAGNIK-WNQHRDIWYEDLMKV-AGTVCAPKEMGAEEALFILYTSGSTGKP 266
                                                    998**************76.**************5.**************************** PP

                                      TIGR02188 255 kGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivygPLanGattllfegvpt 318
                                                    kGv+htt+Gyll+aalt++ vfd+k++d++wCtaDvGWvtGhsYivygPLanGattllfegvp+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5659 267 KGVQHTTAGYLLYAALTHERVFDYKPGDVYWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPN 330
                                                    **************************************************************** PP

                                      TIGR02188 319 ypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyy 382
                                                    ypd  r+++v++k+kv+i+YtaPtaiRa+m+ g+++v+  d sslr+lgsvGepinpeaw+Wyy
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5659 331 YPDITRVAKVVDKHKVNILYTAPTAIRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYY 394
                                                    **************************************************************** PP

                                      TIGR02188 383 evvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeg 446
                                                    ++vGke+cpivdtwWqtetGg+li+plpg at+lkpgsat+P+fG+ +++vd+ g+ +e  +e 
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5659 395 KNVGKERCPIVDTWWQTETGGVLISPLPG-ATALKPGSATRPFFGVVPALVDNLGNLIEGAAE- 456
                                                    *****************************.6****************************8777. PP

                                      TIGR02188 447 gvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGh 510
                                                    g Lvi ++wP+++rt+ygd++rfv+tYfk+++g+yftGDgarrd+dGy+wi+GRvDdv+nvsGh
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5659 457 GNLVILDSWPGQARTLYGDHDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGH 520
                                                    79************************************************************** PP

                                      TIGR02188 511 rlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeig 574
                                                    r+gtaeiesa+v+h++vaeaavvgvp++ikg+ i+++v+l++g+e++e +l+ elk++vrkeig
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5659 521 RMGTAEIESAMVAHPKVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSE-ALRLELKNWVRKEIG 583
                                                    *********************************************999.6************** PP

                                      TIGR02188 575 piakpdkilvveelPktRsGkimRRllrkiaege.ellgdvstledpsvveelke 628
                                                    pia+pd i++++ lPktRsGkimRR+lrkia+ e + lgd+stl+dpsvv++l+e
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5659 584 PIASPDVIQWAPGLPKTRSGKIMRRILRKIATAEyDGLGDISTLADPSVVAHLIE 638
                                                    **********************************9****************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (646 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: 0.02u 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 11.73
//
[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