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_4702 PP_4702 acetyl-CoA synthetase

Query= reanno::pseudo3_N2E3:AO353_03060
         (651 letters)



>FitnessBrowser__Putida:PP_4702
          Length = 644

 Score =  861 bits (2224), Expect = 0.0
 Identities = 408/637 (64%), Positives = 491/637 (77%), Gaps = 4/637 (0%)

Query: 7   YPVRPEVAANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHVD 66
           YP    V+ +       Y+ +Y+QSV +PD FW EQAKRLDWIKP+++V+Q   D H   
Sbjct: 7   YPQALAVSQSAALTPEDYRRLYRQSVEDPDTFWAEQAKRLDWIKPWSSVQQC--DLHTGK 64

Query: 67  IKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPAESRNITYRELHEQVCKFANALRG 126
            +WF    LNVSYNC+DRHLA+RG+Q A++WEGDDP +S+ ITYRELH QVC+ ANA++ 
Sbjct: 65  ARWFDGAQLNVSYNCIDRHLAQRGEQTALLWEGDDPKDSKAITYRELHRQVCRLANAMKA 124

Query: 127 QDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVITA 186
           + V +GD V+IYMPMIPEA  AMLACTRIGAIHSVVFGGFSP+AL  RI+D   + VITA
Sbjct: 125 RGVKKGDRVSIYMPMIPEAAFAMLACTRIGAIHSVVFGGFSPDALRDRILDADCRTVITA 184

Query: 187 DEGLRAGKKISLKANVDDALTNPETSSIQKVIVCKRTGGNIKWNQHRDIWYEDLMKVAGT 246
           DEG+R GK+I LK NVD AL +    ++  V+V +RTGG++ W + RD+WY +  K AG 
Sbjct: 185 DEGVRGGKRIPLKQNVDKALAS--CPAVSSVLVVRRTGGDVAWTEGRDLWYHEATKDAGD 242

Query: 247 VCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAALTHERVFDYRPGEIYWCTAD 306
            C P+ M AE+ LFILYTSGSTGKPKGV HTTGGYLL A +T + VFDYR GE++WCTAD
Sbjct: 243 DCPPEPMEAEDPLFILYTSGSTGKPKGVLHTTGGYLLQATMTFKVVFDYRDGEVFWCTAD 302

Query: 307 VGWVTGHTYIVYGPLANGATTLLFEGVPNYPDITRVAKIIDKHKVNILYTAPTAIRAMMA 366
           VGWVTGH+YIVYGPLANGA +L+FEGVPNYPD +R  +++DKH+VNI YTAPTA+RA+M 
Sbjct: 303 VGWVTGHSYIVYGPLANGAISLMFEGVPNYPDTSRFWQVVDKHQVNIFYTAPTALRALMR 362

Query: 367 QGTAAVEGADGSSLRLLGSVGEPINPEAWEWYYKNVGQSRCPIVDTWWQTETGATLMSPL 426
           +G+A ++     SLRLLGSVGEPINPEAWEWY++ VGQ RCPIVDTWWQTETG  +++PL
Sbjct: 363 EGSAPLQSTSRKSLRLLGSVGEPINPEAWEWYFEEVGQKRCPIVDTWWQTETGGIMLTPL 422

Query: 427 PGAHGLKPGSAARPFFGVVPALVDNLGNIIEGVAEGNLVILDSWPGQARTLYGDHDRFVD 486
           PG   LKPG A +P FGV P L+D  G +IEG   G L I  SWPGQ R++YGDH R VD
Sbjct: 423 PGTQSLKPGCATQPMFGVQPVLLDEKGKLIEGPGAGVLAIKASWPGQIRSVYGDHQRMVD 482

Query: 487 TYFKTFRGMYFTGDGARRDADGYWWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAEAA 546
           TYFK   G YFTGDGARRDADG +WITGR+DDV+NVSGHR+GTAE+ESA+V H  VAEAA
Sbjct: 483 TYFKPLPGYYFTGDGARRDADGDYWITGRIDDVINVSGHRIGTAEVESALVLHDSVAEAA 542

Query: 547 VVGVPHDIKGQGIYVYVTLNGGEEPSEALRLELKNWVRKEIGPIASPDVIQWAPGLPKTR 606
           VVG PHD+KGQG+Y +VT   G  P + L+ EL   V KEIG  A P++IQWAP LPKTR
Sbjct: 543 VVGYPHDLKGQGVYAFVTTMNGVTPDDTLKAELLALVSKEIGSFAKPELIQWAPALPKTR 602

Query: 607 SGKIMRRILRKIATGEYDGLGDISTLADPGVVQHLID 643
           SGKIMRRILRKIA  E + LGD STLADP VVQ LID
Sbjct: 603 SGKIMRRILRKIACNELENLGDTSTLADPSVVQGLID 639


Lambda     K      H
   0.319    0.136    0.425 

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: 1451
Number of extensions: 70
Number of successful extensions: 3
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: 644
Length adjustment: 38
Effective length of query: 613
Effective length of database: 606
Effective search space:   371478
Effective search space used:   371478
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 PP_4702 PP_4702 (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.7367.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 1039.4   0.0          0 1039.2   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_4702  PP_4702 acetyl-CoA synthetase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_4702  PP_4702 acetyl-CoA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1039.2   0.0         0         0       4     628 ..      21     639 ..      18     640 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1039.2 bits;  conditional E-value: 0
                           TIGR02188   4 leeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgelnvsyncvdrhvekrkdkvaii 77 
                                          e+y++ly++++edp++fwa++ak+ l+w+kp+++v++++l++ k++Wf++++lnvsync+drh+++r +++a+ 
  lcl|FitnessBrowser__Putida:PP_4702  21 PEDYRRLYRQSVEDPDTFWAEQAKR-LDWIKPWSSVQQCDLHTgKARWFDGAQLNVSYNCIDRHLAQRGEQTALL 94 
                                         689*********************5.***************999******************************* PP

                           TIGR02188  78 wegdeegedsrkltYaellrevcrlanvlkelGvkkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaea 152
                                         wegd+++ ds+++tY+el+r+vcrlan++k+ Gvkkgdrv+iY+pmipea++amlac+RiGa+hsvvf+Gfs++a
  lcl|FitnessBrowser__Putida:PP_4702  95 WEGDDPK-DSKAITYRELHRQVCRLANAMKARGVKKGDRVSIYMPMIPEAAFAMLACTRIGAIHSVVFGGFSPDA 168
                                         ******9.5****************************************************************** PP

                           TIGR02188 153 laeRivdaeaklvitadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwweelvekea 227
                                         l++Ri da++++vitadeg+Rggk+i+lk++vd+al++++ +v++vlvv+rtg +va w+egrD+w++e++++ a
  lcl|FitnessBrowser__Putida:PP_4702 169 LRDRILDADCRTVITADEGVRGGKRIPLKQNVDKALASCP-AVSSVLVVRRTGGDVA-WTEGRDLWYHEATKD-A 240
                                         ***************************************9.7*************77.**************7.* PP

                           TIGR02188 228 saecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvfdikdedifwCtaDvGWvtGhsYivyg 302
                                          ++c+pe++++edplfiLYtsGstGkPkGvlhttgGyll+a++t+k+vfd++d+++fwCtaDvGWvtGhsYivyg
  lcl|FitnessBrowser__Putida:PP_4702 241 GDDCPPEPMEAEDPLFILYTSGSTGKPKGVLHTTGGYLLQATMTFKVVFDYRDGEVFWCTADVGWVTGHSYIVYG 315
                                         *************************************************************************** PP

                           TIGR02188 303 PLanGattllfegvptypdasrfweviekykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpea 377
                                         PLanGa +l+fegvp+ypd+srfw+v++k++v+ifYtaPta+Ralm++g++ +++++++slr+lgsvGepinpea
  lcl|FitnessBrowser__Putida:PP_4702 316 PLANGAISLMFEGVPNYPDTSRFWQVVDKHQVNIFYTAPTALRALMREGSAPLQSTSRKSLRLLGSVGEPINPEA 390
                                         *************************************************************************** PP

                           TIGR02188 378 weWyyevvGkekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeveeeeeggvLvik 452
                                         weWy+e+vG+++cpivdtwWqtetGgi++tplpg + +lkpg+at+P+fG++++++de+gk +e     gvL+ik
  lcl|FitnessBrowser__Putida:PP_4702 391 WEWYFEEVGQKRCPIVDTWWQTETGGIMLTPLPG-TQSLKPGCATQPMFGVQPVLLDEKGKLIEGPGA-GVLAIK 463
                                         **********************************.6***************************97666.8***** PP

                           TIGR02188 453 kpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiwilGRvDdvinvsGhrlgtaeiesalvsheav 527
                                          +wP+++r++ygd++r+v+tYfk l+g+yftGDgarrd+dG++wi+GR+DdvinvsGhr+gtae+esalv h++v
  lcl|FitnessBrowser__Putida:PP_4702 464 ASWPGQIRSVYGDHQRMVDTYFKPLPGYYFTGDGARRDADGDYWITGRIDDVINVSGHRIGTAEVESALVLHDSV 538
                                         *************************************************************************** PP

                           TIGR02188 528 aeaavvgvpdeikgeaivafvvlkegveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllr 602
                                         aeaavvg+p+++kg+ ++afv+ ++gv++d++ l++el +lv+keig++akp+ i+++++lPktRsGkimRR+lr
  lcl|FitnessBrowser__Putida:PP_4702 539 AEAAVVGYPHDLKGQGVYAFVTTMNGVTPDDT-LKAELLALVSKEIGSFAKPELIQWAPALPKTRSGKIMRRILR 612
                                         *******************************5.****************************************** PP

                           TIGR02188 603 kiaege.ellgdvstledpsvveelke 628
                                         kia +e e+lgd+stl+dpsvv+ l++
  lcl|FitnessBrowser__Putida:PP_4702 613 KIACNElENLGDTSTLADPSVVQGLID 639
                                         **********************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (644 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: 00:00:00.04
# Mc/sec: 8.39
//
[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