Alignments for a candidate for paaK in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaK in Klebsiella michiganensis M5al

Align Phenylacetate-coenzyme A ligase; Phenylacetyl-CoA ligase; PA-CoA ligase; EC 6.2.1.30 (characterized)
to candidate BWI76_RS13140 BWI76_RS13140 phenylacetate-CoA ligase

Query= SwissProt::P76085
         (437 letters)



>FitnessBrowser__Koxy:BWI76_RS13140
          Length = 438

 Score =  829 bits (2141), Expect = 0.0
 Identities = 403/432 (93%), Positives = 418/432 (96%)

Query: 1   MITNTKLDPIETASVDELQALQTQRLKWTLKHAYENVPMYRRKFDAAGVHPDDFRELSDL 60
           M T T+LDPIE+AS DELQALQTQRLKWTLKHAY+NVPMYRRKFDAAGVHPDDF ELSDL
Sbjct: 1   MTTITQLDPIESASRDELQALQTQRLKWTLKHAYDNVPMYRRKFDAAGVHPDDFHELSDL 60

Query: 61  RKFPCTTKQDLRDNYPFDTFAVPMEQVVRIHASSGTTGKPTVVGYTQNDIDNWANIVARS 120
            KFPCTTKQDLRDNYPFDTFAVPMEQVVRIHASSGTTGKPTVVGYTQNDIDNWANIVARS
Sbjct: 61  SKFPCTTKQDLRDNYPFDTFAVPMEQVVRIHASSGTTGKPTVVGYTQNDIDNWANIVARS 120

Query: 121 LRAAGGSPKDKIHVAYGYGLFTGGLGAHYGAERLGATVIPMSGGQTEKQAQLIRDFQPDM 180
           LRAAGG+ KDKIHVAYGYGLFTGGLGAHYGAERLGATVIPMSGGQTEKQAQLIRDF+PDM
Sbjct: 121 LRAAGGTAKDKIHVAYGYGLFTGGLGAHYGAERLGATVIPMSGGQTEKQAQLIRDFKPDM 180

Query: 181 IMVTPSYCLNLIEELERQLGGDASGCSLRVGVFGAEPWTQAMRKEIERRLGITALDIYGL 240
           IMVTPSYCLNLIEELERQ+GGDASGCSLRVGVFGAEPWT+AMR EIERRLGI+ALDIYGL
Sbjct: 181 IMVTPSYCLNLIEELERQMGGDASGCSLRVGVFGAEPWTRAMRTEIERRLGISALDIYGL 240

Query: 241 SEVMGPGVAMECLETTDGPTIWEDHFYPEIVNPHDGTPLADGEHGELLFTTLTKEALPVI 300
           SEVMGPGVAMECLET DGPTIWEDHFYPE+VNP +GTPL DGEHGELLFTTLTKEALPVI
Sbjct: 241 SEVMGPGVAMECLETADGPTIWEDHFYPEVVNPDNGTPLTDGEHGELLFTTLTKEALPVI 300

Query: 301 RYRTRDLTRLLPGTARTMRRMDRISGRSDDMLIIRGVNVFPSQLEEEIVKFEHLSPHYQL 360
           RYRTRDLTRLLPGTARTMRRMDRISGRSDDMLIIRGVNVFPSQLEEEI+KFEHL+PHYQL
Sbjct: 301 RYRTRDLTRLLPGTARTMRRMDRISGRSDDMLIIRGVNVFPSQLEEEILKFEHLAPHYQL 360

Query: 361 EVNRRGHLDSLSVKVELKESSLTLTHEQRCQVCHQLRHRIKSMVGISTDVMIVNCGSIPR 420
           EVNRRGHLDSLSV+VELKES L L HEQRCQ+CHQLRHRIKSMVGISTD+ IVNCGSIPR
Sbjct: 361 EVNRRGHLDSLSVRVELKESGLALNHEQRCQICHQLRHRIKSMVGISTDISIVNCGSIPR 420

Query: 421 SEGKACRVFDLR 432
           SEGKACRVFDLR
Sbjct: 421 SEGKACRVFDLR 432


Lambda     K      H
   0.320    0.137    0.411 

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: 774
Number of extensions: 24
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: 437
Length of database: 438
Length adjustment: 32
Effective length of query: 405
Effective length of database: 406
Effective search space:   164430
Effective search space used:   164430
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 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate BWI76_RS13140 BWI76_RS13140 (phenylacetate-CoA ligase)
to HMM TIGR02155 (paaF: phenylacetate-CoA ligase (EC 6.2.1.30))

# 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/TIGR02155.hmm
# target sequence database:        /tmp/gapView.5416.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02155  [M=422]
Accession:   TIGR02155
Description: PA_CoA_ligase: phenylacetate-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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   8.5e-238  774.8   0.0   9.6e-238  774.6   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS13140  BWI76_RS13140 phenylacetate-CoA 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS13140  BWI76_RS13140 phenylacetate-CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  774.6   0.0  9.6e-238  9.6e-238       1     422 []      11     432 ..      11     432 .. 0.99

  Alignments for each domain:
  == domain 1  score: 774.6 bits;  conditional E-value: 9.6e-238
                               TIGR02155   1 eklsldelralqlerlkvsvkrayenvpayrkafdaagvkpddlkelsdlakfpltaksdlrdnypfdlla 71 
                                             e++s+del+alq++rlk+++k+ay+nvp+yr++fdaagv+pdd++elsdl kfp+t+k+dlrdnypfd++a
  lcl|FitnessBrowser__Koxy:BWI76_RS13140  11 ESASRDELQALQTQRLKWTLKHAYDNVPMYRRKFDAAGVHPDDFHELSDLSKFPCTTKQDLRDNYPFDTFA 81 
                                             789******************************************************************** PP

                               TIGR02155  72 vprekvvrvhassGttGkptvvaytqkdldtwsevvarslraaGGrkgdllhnayGyGlftGGlGvhyGae 142
                                             vp+e+vvr+hassGttGkptvv+ytq+d+d+w+++varslraaGG ++d++h+ayGyGlftGGlG+hyGae
  lcl|FitnessBrowser__Koxy:BWI76_RS13140  82 VPMEQVVRIHASSGTTGKPTVVGYTQNDIDNWANIVARSLRAAGGTAKDKIHVAYGYGLFTGGLGAHYGAE 152
                                             *********************************************************************** PP

                               TIGR02155 143 klGatvvpisGGqtekqvqliqdfkpdiiavtpsyilalleelkrlg.idpedislkvailGaepwteamr 212
                                             +lGatv+p+sGGqtekq+qli+dfkpd+i+vtpsy+l+l+eel+r+   d++ +sl+v+++Gaepwt+amr
  lcl|FitnessBrowser__Koxy:BWI76_RS13140 153 RLGATVIPMSGGQTEKQAQLIRDFKPDMIMVTPSYCLNLIEELERQMgGDASGCSLRVGVFGAEPWTRAMR 223
                                             ********************************************97549********************** PP

                               TIGR02155 213 kelearlgikaldiyGlseviGpGvanecvetkdGlviwedhfypeiidpetgevlpdGeeGelvfttltk 283
                                             +e+e+rlgi+aldiyGlsev+GpGva+ec+et dG++iwedhfype+++p++g++l+dGe+Gel+fttltk
  lcl|FitnessBrowser__Koxy:BWI76_RS13140 224 TEIERRLGISALDIYGLSEVMGPGVAMECLETADGPTIWEDHFYPEVVNPDNGTPLTDGEHGELLFTTLTK 294
                                             *********************************************************************** PP

                               TIGR02155 284 ealpviryrtrdltrllpgtartmrrmdkikGrsddllilrGvnvfptqleevllkldklsphyqleltre 354
                                             ealpviryrtrdltrllpgtartmrrmd+i+Grsdd+li+rGvnvfp+qlee +lk+++l+phyqle++r+
  lcl|FitnessBrowser__Koxy:BWI76_RS13140 295 EALPVIRYRTRDLTRLLPGTARTMRRMDRISGRSDDMLIIRGVNVFPSQLEEEILKFEHLAPHYQLEVNRR 365
                                             *********************************************************************** PP

                               TIGR02155 355 GaldeltlkvelkdesaalrlleqksllakkiekkikaevgvsvdvelvepgslerseGkakrvvdkr 422
                                             G+ld+l+++velk es  + ++eq+++++++++++ik++vg+s+d+++v++gs++rseGka+rv+d+r
  lcl|FitnessBrowser__Koxy:BWI76_RS13140 366 GHLDSLSVRVELK-ESGLALNHEQRCQICHQLRHRIKSMVGISTDISIVNCGSIPRSEGKACRVFDLR 432
                                             *************.7888888*********************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (422 nodes)
Target sequences:                          1  (438 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 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 9.43
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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 (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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources