GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acs in Pseudomonas fluorescens GW456-L13

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate PfGW456L13_1517 Acetyl-coenzyme A synthetase (EC 6.2.1.1)

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



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517
           Acetyl-coenzyme A synthetase (EC 6.2.1.1)
          Length = 645

 Score =  815 bits (2104), Expect = 0.0
 Identities = 400/641 (62%), Positives = 481/641 (75%), Gaps = 7/641 (1%)

Query: 5   SLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKR-LDWIKPFTTVKQTSFDDH 63
           S +P    V  +    +  Y+ +Y+QSV +P  FW EQA R LDW  P+ TV++ +    
Sbjct: 5   STFPKADAVRRAAQLSQDDYQRLYRQSVEHPSTFWAEQATRFLDWSAPWETVQRYNLKTG 64

Query: 64  HVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANA 123
             +  WFA   LNVSYNC+DRHL +RGDQ+AIIWEGDDP++S +ITY++LHE VC+ AN 
Sbjct: 65  --EASWFAGAQLNVSYNCIDRHLEKRGDQVAIIWEGDDPADSTSITYKKLHENVCRLANV 122

Query: 124 LRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVV 183
           L+ + V +GD V IYMPMIPEA  AMLACTRIGA+HSVVFGGFSP++L  RI+D   + V
Sbjct: 123 LKNRGVKKGDRVCIYMPMIPEAAYAMLACTRIGAVHSVVFGGFSPDSLRDRILDADCRTV 182

Query: 184 ITADEGVRAGKKIPLKANVDDALTN-PETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMK 242
           ITADEGVR GK + LK NVD AL + P+ SS   V+V +RT G + W + RDI Y+  ++
Sbjct: 183 ITADEGVRGGKVVSLKQNVDKALQSCPDVSS---VLVVERTKGLVNWVEGRDIKYQQALR 239

Query: 243 VAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYW 302
            A   C P+ M AE+ LFILYTSGSTGKPKGV HTT GYLL AA+T + V DY+  EV+W
Sbjct: 240 EASADCPPEPMDAEDPLFILYTSGSTGKPKGVLHTTGGYLLQAAMTFKYVLDYRDDEVFW 299

Query: 303 CTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIR 362
           CTADVGWVTGHSYIVYGPLANGATTL+FEGVPNYP  +R  +VIDKHKV+I YTAPTA+R
Sbjct: 300 CTADVGWVTGHSYIVYGPLANGATTLIFEGVPNYPSTSRFWQVIDKHKVNIFYTAPTALR 359

Query: 363 AMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVL 422
           A+M  G   ++    +S+RLLG+VGEPINPEAW+WY+  VG+ERCPIVDTWWQTETGG++
Sbjct: 360 ALMREGPEPLKQTSRASVRLLGTVGEPINPEAWEWYFHEVGEERCPIVDTWWQTETGGIM 419

Query: 423 ISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHD 482
           +SPL  A  +KPG AT+P FGV P L+D  G  I+GA  G L I  SWP Q R++Y D  
Sbjct: 420 LSPLVSAQRIKPGCATQPMFGVQPVLLDEQGKEIKGAGSGVLAIKSSWPAQIRSVYRDPQ 479

Query: 483 RFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKV 542
           R VDTYFK + G YFTGDGARRDEDG YWITGR+DDV+NVSGHR+GTAE+ESA+V H  +
Sbjct: 480 RMVDTYFKPYPGYYFTGDGARRDEDGDYWITGRIDDVINVSGHRIGTAEVESALVLHENI 539

Query: 543 AEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGL 602
           AEAA VG PHDIKGQGIYV+VT   G ET++ L+ EL   V KEIG  A PD+IQWAP L
Sbjct: 540 AEAAAVGYPHDIKGQGIYVFVTPMNGVETNDELKKELLALVSKEIGSFAKPDLIQWAPAL 599

Query: 603 PKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIE 643
           PKTRSGKIMRRILRKIA  E D LGD STLADP VV  LI+
Sbjct: 600 PKTRSGKIMRRILRKIACNELDNLGDTSTLADPSVVQGLID 640


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: 1339
Number of extensions: 73
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: 645
Length adjustment: 38
Effective length of query: 613
Effective length of database: 607
Effective search space:   372091
Effective search space used:   372091
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 PfGW456L13_1517 (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.28299.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 1018.1   0.0          0 1017.9   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517  Acetyl-coenzyme A synthetase (EC


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517  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 ! 1017.9   0.0         0         0       3     628 ..      20     640 ..      18     641 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1017.9 bits;  conditional E-value: 0
                                               TIGR02188   3 eleeykelyeeaiedpekfwaklakeelewlkpfekvldeslep.kvkWfedgel 56 
                                                             ++++y++ly++++e+p++fwa++a++ l+w  p+e+v++ +l++ ++ Wf++++l
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517  20 SQDDYQRLYRQSVEHPSTFWAEQATRFLDWSAPWETVQRYNLKTgEASWFAGAQL 74 
                                                             5789*************************************9999********** PP

                                               TIGR02188  57 nvsyncvdrhvekrkdkvaiiwegdeegedsrkltYaellrevcrlanvlkelGv 111
                                                             nvsync+drh+ekr d+vaiiwegd++  ds ++tY++l+++vcrlanvlk+ Gv
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517  75 NVSYNCIDRHLEKRGDQVAIIWEGDDPA-DSTSITYKKLHENVCRLANVLKNRGV 128
                                                             ***************************9.5************************* PP

                                               TIGR02188 112 kkgdrvaiYlpmipeaviamlacaRiGavhsvvfaGfsaealaeRivdaeaklvi 166
                                                             kkgdrv+iY+pmipea++amlac+RiGavhsvvf+Gfs+++l++Ri da++++vi
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517 129 KKGDRVCIYMPMIPEAAYAMLACTRIGAVHSVVFGGFSPDSLRDRILDADCRTVI 183
                                                             ******************************************************* PP

                                               TIGR02188 167 tadeglRggkvielkkivdealekaeesvekvlvvkrtgeevaewkegrDvwwee 221
                                                             tadeg+Rggkv++lk++vd+al++++ +v++vlvv+rt+  v+ w+egrD+++++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517 184 TADEGVRGGKVVSLKQNVDKALQSCP-DVSSVLVVERTKGLVN-WVEGRDIKYQQ 236
                                                             *************************9.6**********99955.*********** PP

                                               TIGR02188 222 lvekeasaecepekldsedplfiLYtsGstGkPkGvlhttgGylllaaltvkyvf 276
                                                             ++++ asa+c+pe++d+edplfiLYtsGstGkPkGvlhttgGyll+aa+t+kyv 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517 237 ALRE-ASADCPPEPMDAEDPLFILYTSGSTGKPKGVLHTTGGYLLQAAMTFKYVL 290
                                                             ***6.************************************************** PP

                                               TIGR02188 277 dikdedifwCtaDvGWvtGhsYivygPLanGattllfegvptypdasrfweviek 331
                                                             d++d+++fwCtaDvGWvtGhsYivygPLanGattl+fegvp+yp++srfw+vi+k
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517 291 DYRDDEVFWCTADVGWVTGHSYIVYGPLANGATTLIFEGVPNYPSTSRFWQVIDK 345
                                                             ******************************************************* PP

                                               TIGR02188 332 ykvtifYtaPtaiRalmklgeelvkkhdlsslrvlgsvGepinpeaweWyyevvG 386
                                                             +kv+ifYtaPta+Ralm++g e +k++++ s+r+lg+vGepinpeaweWy+++vG
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517 346 HKVNIFYTAPTALRALMREGPEPLKQTSRASVRLLGTVGEPINPEAWEWYFHEVG 400
                                                             ******************************************************* PP

                                               TIGR02188 387 kekcpivdtwWqtetGgilitplpgvatelkpgsatlPlfGieaevvdeegkeve 441
                                                             +e+cpivdtwWqtetGgi+++pl + a  +kpg+at+P+fG++++++de+gke++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517 401 EERCPIVDTWWQTETGGIMLSPLVS-AQRIKPGCATQPMFGVQPVLLDEQGKEIK 454
                                                             *************************.6***************************9 PP

                                               TIGR02188 442 eeeeggvLvikkpwPsmlrtiygdeerfvetYfkklkglyftGDgarrdkdGyiw 496
                                                                + gvL+ik++wP+++r++y+d++r+v+tYfk ++g+yftGDgarrd+dG++w
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517 455 GAGS-GVLAIKSSWPAQIRSVYRDPQRMVDTYFKPYPGYYFTGDGARRDEDGDYW 508
                                                             8777.8************************************************* PP

                                               TIGR02188 497 ilGRvDdvinvsGhrlgtaeiesalvsheavaeaavvgvpdeikgeaivafvvlk 551
                                                             i+GR+DdvinvsGhr+gtae+esalv he++aeaa+vg+p++ikg+ i++fv+ +
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517 509 ITGRIDDVINVSGHRIGTAEVESALVLHENIAEAAAVGYPHDIKGQGIYVFVTPM 563
                                                             ******************************************************* PP

                                               TIGR02188 552 egveedeeelekelkklvrkeigpiakpdkilvveelPktRsGkimRRllrkiae 606
                                                             +gve+++e l+kel +lv+keig++akpd i+++++lPktRsGkimRR+lrkia 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517 564 NGVETNDE-LKKELLALVSKEIGSFAKPDLIQWAPALPKTRSGKIMRRILRKIAC 617
                                                             ******95.********************************************** PP

                                               TIGR02188 607 ge.ellgdvstledpsvveelke 628
                                                             +e ++lgd+stl+dpsvv+ l++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517 618 NElDNLGDTSTLADPSVVQGLID 640
                                                             ******************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (629 nodes)
Target sequences:                          1  (645 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: 8.55
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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