GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Pseudomonas putida KT2440

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate PP_4487 PP_4487 acetyl-CoA synthetase

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



>FitnessBrowser__Putida:PP_4487
          Length = 696

 Score = 1243 bits (3216), Expect = 0.0
 Identities = 597/651 (91%), Positives = 623/651 (95%)

Query: 1   MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60
           MSAA LYPVRPEVAA+TLTDEATYKAMYQQSV+NPDGFWREQA+R+DWIKPFT VKQTSF
Sbjct: 44  MSAAPLYPVRPEVAATTLTDEATYKAMYQQSVINPDGFWREQAQRIDWIKPFTKVKQTSF 103

Query: 61  DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKF 120
           DDHHVDIKWFADGTLNVS NCLDRHL ERGDQ+AIIWEGDDPSE RNITYRELHE+VCKF
Sbjct: 104 DDHHVDIKWFADGTLNVSSNCLDRHLEERGDQLAIIWEGDDPSEHRNITYRELHEQVCKF 163

Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180
           ANALRGQDVHRGDVVTIYMPMIPEAVVAMLAC RIGAIHSVVFGGFSPEALAGRIIDCKS
Sbjct: 164 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACARIGAIHSVVFGGFSPEALAGRIIDCKS 223

Query: 181 KVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDL 240
           KVVITADEGVR G++ PLKANVD ALTNPETSS+QK+IVCKRT G+I W+QHRDIWYEDL
Sbjct: 224 KVVITADEGVRGGRRTPLKANVDLALTNPETSSVQKIIVCKRTGGDIAWHQHRDIWYEDL 283

Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEV 300
           MKVA + CAPKEMGAEEALFILYTSGSTGKPKGV HTT GYL+YAALTHERVFDY+PGEV
Sbjct: 284 MKVASSHCAPKEMGAEEALFILYTSGSTGKPKGVLHTTGGYLVYAALTHERVFDYRPGEV 343

Query: 301 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTA 360
           YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRV+K++DKHKV+ILYTAPTA
Sbjct: 344 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVSKIVDKHKVNILYTAPTA 403

Query: 361 IRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGG 420
           IRAMMA G AAVEGADGSSLRLLGSVGEPINPEAW+WYYK VGKERCPIVDTWWQTETGG
Sbjct: 404 IRAMMAEGQAAVEGADGSSLRLLGSVGEPINPEAWNWYYKTVGKERCPIVDTWWQTETGG 463

Query: 421 VLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGD 480
           +LISPLPGAT LKPGSATRPFFGVVPALVDNLGNLI+GAAEGNLVILDSWPGQ+R+LYGD
Sbjct: 464 ILISPLPGATGLKPGSATRPFFGVVPALVDNLGNLIDGAAEGNLVILDSWPGQSRSLYGD 523

Query: 481 HDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540
           HDRFVDTYFKTF GMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAH 
Sbjct: 524 HDRFVDTYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHS 583

Query: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAP 600
           KVAEAAVVGVPHDIKGQGIYVYVTLNAG E SE LRLELKNWVRKEIGPIASPDVIQWAP
Sbjct: 584 KVAEAAVVGVPHDIKGQGIYVYVTLNAGIEASEQLRLELKNWVRKEIGPIASPDVIQWAP 643

Query: 601 GLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIETHKTMNVA 651
           GLPKTRSGKIMRRILRKIAT EYD LGDISTLADPGVV HLI+THK MN+A
Sbjct: 644 GLPKTRSGKIMRRILRKIATGEYDALGDISTLADPGVVQHLIDTHKAMNLA 694


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: 1751
Number of extensions: 57
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: 696
Length adjustment: 39
Effective length of query: 612
Effective length of database: 657
Effective search space:   402084
Effective search space used:   402084
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 PP_4487 PP_4487 (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.31929.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 1018.9   0.1          0 1018.6   0.1    1.0  1  lcl|FitnessBrowser__Putida:PP_4487  PP_4487 acetyl-CoA synthetase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_4487  PP_4487 acetyl-CoA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1018.6   0.1         0         0       3     628 ..      63     686 ..      61     687 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1018.6 bits;  conditional E-value: 0
                           TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep...kvkWfedgelnvsyncvdrhvekrkdkv 74 
                                         +  +yk++y++++ +p+ fw+++a+ +++w+kpf+kv+++s+++   ++kWf+dg+lnvs nc+drh+e+r d++
  lcl|FitnessBrowser__Putida:PP_4487  63 DEATYKAMYQQSVINPDGFWREQAQ-RIDWIKPFTKVKQTSFDDhhvDIKWFADGTLNVSSNCLDRHLEERGDQL 136
                                         5679*********************.5*************99887789*************************** PP

                           TIGR02188  75 aiiwegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfs 149
                                         aiiwegd+++e +r++tY+el+++vc++an+l+ + v++gd v+iY+pmipeav+amlacaRiGa+hsvvf+Gfs
  lcl|FitnessBrowser__Putida:PP_4487 137 AIIWEGDDPSE-HRNITYRELHEQVCKFANALRGQDVHRGDVVTIYMPMIPEAVVAMLACARIGAIHSVVFGGFS 210
                                         *********96.*************************************************************** PP

                           TIGR02188 150 aealaeRivdaeaklvitadeglRggkvielkkivdealekaee.svekvlvvkrtgeevaewkegrDvwweelv 223
                                         +eala Ri+d+++k+vitadeg+Rgg++++lk++vd al++ e+ sv+k++v+krtg ++a w++ rD+w+e+l+
  lcl|FitnessBrowser__Putida:PP_4487 211 PEALAGRIIDCKSKVVITADEGVRGGRRTPLKANVDLALTNPETsSVQKIIVCKRTGGDIA-WHQHRDIWYEDLM 284
                                         *****************************************9998**************77.************* PP

                           TIGR02188 224 ekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsY 298
                                         +  as++c+p+++++e+ lfiLYtsGstGkPkGvlhttgGyl++aalt++ vfd+++++++wCtaDvGWvtGhsY
  lcl|FitnessBrowser__Putida:PP_4487 285 KV-ASSHCAPKEMGAEEALFILYTSGSTGKPKGVLHTTGGYLVYAALTHERVFDYRPGEVYWCTADVGWVTGHSY 358
                                         *5.************************************************************************ PP

                           TIGR02188 299 ivygPLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepi 373
                                         ivygPLanGattllfegvp+ypd  r+ ++++k+kv+i+YtaPtaiRa+m++g+++v+  d sslr+lgsvGepi
  lcl|FitnessBrowser__Putida:PP_4487 359 IVYGPLANGATTLLFEGVPNYPDITRVSKIVDKHKVNILYTAPTAIRAMMAEGQAAVEGADGSSLRLLGSVGEPI 433
                                         *************************************************************************** PP

                           TIGR02188 374 npeaweWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggv 448
                                         npeaw+Wyy++vGke+cpivdtwWqtetGgili+plpg at lkpgsat+P+fG+ +++vd+ g+ ++  +e g 
  lcl|FitnessBrowser__Putida:PP_4487 434 NPEAWNWYYKTVGKERCPIVDTWWQTETGGILISPLPG-ATGLKPGSATRPFFGVVPALVDNLGNLIDGAAE-GN 506
                                         **************************************.6****************************8777.79 PP

                           TIGR02188 449 LvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvs 523
                                         Lvi ++wP++ r++ygd++rfv+tYfk+++g+yftGDgarrd+dGy+wi+GRvDdv+nvsGhr+gtaeiesa+v+
  lcl|FitnessBrowser__Putida:PP_4487 507 LVILDSWPGQSRSLYGDHDRFVDTYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVA 581
                                         *************************************************************************** PP

                           TIGR02188 524 heavaeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimR 598
                                         h++vaeaavvgvp++ikg+ i+++v+l++g+e++e +l+ elk++vrkeigpia+pd i++++ lPktRsGkimR
  lcl|FitnessBrowser__Putida:PP_4487 582 HSKVAEAAVVGVPHDIKGQGIYVYVTLNAGIEASE-QLRLELKNWVRKEIGPIASPDVIQWAPGLPKTRSGKIMR 655
                                         ********************************999.6************************************** PP

                           TIGR02188 599 Rllrkiaege.ellgdvstledpsvveelke 628
                                         R+lrkia+ge ++lgd+stl+dp vv++l++
  lcl|FitnessBrowser__Putida:PP_4487 656 RILRKIATGEyDALGDISTLADPGVVQHLID 686
                                         ***************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (696 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: 00:00:00.05
# Mc/sec: 8.08
//
[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