GapMind for catabolism of small carbon sources

 

Aligments for a candidate for paaK in Burkholderia phytofirmans PsJN

Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate BPHYT_RS17360 BPHYT_RS17360 phenylacetate-CoA ligase

Query= BRENDA::B4E7B5
         (432 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS17360 BPHYT_RS17360
           phenylacetate-CoA ligase
          Length = 434

 Score =  802 bits (2071), Expect = 0.0
 Identities = 395/431 (91%), Positives = 416/431 (96%)

Query: 1   MTTPLPLEPIETASRDELTALQLERLKWSLRHAYDHSPVYRRKFDEAGVHPDDLKTLADL 60
           MTT LPL+PIETASRDEL ALQLERLKWSL HAY++SPVYR KFDEAGVHP ++KTLADL
Sbjct: 1   MTTALPLDPIETASRDELAALQLERLKWSLNHAYENSPVYRHKFDEAGVHPSEVKTLADL 60

Query: 61  SRFPFTTKGDLRDSYPFGMFAVPQDRISRIHASSGTTGKPTVVGYTAADIDTWANLVARS 120
           +RFPFTTK DLRDSYPFGMFAVPQ++ISRIHASSGTTGKPTVVGYTA DIDTWANLVARS
Sbjct: 61  ARFPFTTKKDLRDSYPFGMFAVPQEQISRIHASSGTTGKPTVVGYTARDIDTWANLVARS 120

Query: 121 IRAAGARRGDKVHVSYGYGLFTGGLGAHYGAERAGLTVIPFGGGQTEKQVQLIQDFRPDI 180
           +RAAGA+RGDKVH+SYGYGLFTGGLGAHYGAERAGLTVIPFGGGQTEKQVQLIQDFRPDI
Sbjct: 121 VRAAGAKRGDKVHISYGYGLFTGGLGAHYGAERAGLTVIPFGGGQTEKQVQLIQDFRPDI 180

Query: 181 IMVTPSYMLSIADEIERQGLDPVQSSLRIGIFGAEPWTNDMRVAIEQRMGIDAVDIYGLS 240
           IMVTPSYMLSIADE+ERQG+DP   SLRIGIFGAEPWTNDMR AIE+RMGIDAVDIYGLS
Sbjct: 181 IMVTPSYMLSIADELERQGVDPANCSLRIGIFGAEPWTNDMRQAIEKRMGIDAVDIYGLS 240

Query: 241 EVMGPGVASECVETKDGPTIWEDHFYPEIIDPETGEVLPDGELGELVFTSLTKEALPIIR 300
           EVMGPGVASECVETKDGPTIWEDHFYPEIIDPETGEVLPDGELGELVFTSLTKEALPI+R
Sbjct: 241 EVMGPGVASECVETKDGPTIWEDHFYPEIIDPETGEVLPDGELGELVFTSLTKEALPIVR 300

Query: 301 YRTRDLTRLLPGTARTMRRMEKITGRSDDMMIVRGVNVFPTQIEEQLLKQRALAPHYQIV 360
           YRTRDLTRLLPG+ARTMRRMEKITGRSDDMMIVRGVNVFPTQIEE LLKQRALAPHYQIV
Sbjct: 301 YRTRDLTRLLPGSARTMRRMEKITGRSDDMMIVRGVNVFPTQIEELLLKQRALAPHYQIV 360

Query: 361 LTKEGPLDVLTLNVEPCPETAPDTAAIQVAKQALAYDIKSLIGVTAVINVLPVNGIERSV 420
           LTKEGPLDVLTLNVEPCPE+APDTAA+  AKQALAYDIK+LIGV+AV+NVL VNGIERSV
Sbjct: 361 LTKEGPLDVLTLNVEPCPESAPDTAALSTAKQALAYDIKALIGVSAVVNVLAVNGIERSV 420

Query: 421 GKARRVVDKRK 431
           GKARRVVDKRK
Sbjct: 421 GKARRVVDKRK 431


Lambda     K      H
   0.319    0.137    0.404 

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: 773
Number of extensions: 12
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: 432
Length of database: 434
Length adjustment: 32
Effective length of query: 400
Effective length of database: 402
Effective search space:   160800
Effective search space used:   160800
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: 51 (24.3 bits)

Align candidate BPHYT_RS17360 BPHYT_RS17360 (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.16395.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   4.5e-219  713.1   0.0   5.1e-219  712.9   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS17360  BPHYT_RS17360 phenylacetate-CoA 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS17360  BPHYT_RS17360 phenylacetate-CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  712.9   0.0  5.1e-219  5.1e-219       1     422 []      11     430 ..      11     430 .. 0.99

  Alignments for each domain:
  == domain 1  score: 712.9 bits;  conditional E-value: 5.1e-219
                                TIGR02155   1 eklsldelralqlerlkvsvkrayenvpayrkafdaagvkpddlkelsdlakfpltaksdlrdnypfdll 70 
                                              e++s+del alqlerlk+s+++ayen p+yr++fd+agv+p+++k+l+dla+fp+t+k+dlrd ypf+++
  lcl|FitnessBrowser__BFirm:BPHYT_RS17360  11 ETASRDELAALQLERLKWSLNHAYENSPVYRHKFDEAGVHPSEVKTLADLARFPFTTKKDLRDSYPFGMF 80 
                                              89******************************************************************** PP

                                TIGR02155  71 avprekvvrvhassGttGkptvvaytqkdldtwsevvarslraaGGrkgdllhnayGyGlftGGlGvhyG 140
                                              avp+e++ r+hassGttGkptvv+yt++d+dtw+++vars+raaG ++gd++h++yGyGlftGGlG+hyG
  lcl|FitnessBrowser__BFirm:BPHYT_RS17360  81 AVPQEQISRIHASSGTTGKPTVVGYTARDIDTWANLVARSVRAAGAKRGDKVHISYGYGLFTGGLGAHYG 150
                                              ********************************************************************** PP

                                TIGR02155 141 aeklGatvvpisGGqtekqvqliqdfkpdiiavtpsyilalleelkrlgidpedislkvailGaepwtea 210
                                              ae+ G tv+p+ GGqtekqvqliqdf+pdii+vtpsy+l++++el+r+g+dp+++sl+++i+Gaepwt++
  lcl|FitnessBrowser__BFirm:BPHYT_RS17360 151 AERAGLTVIPFGGGQTEKQVQLIQDFRPDIIMVTPSYMLSIADELERQGVDPANCSLRIGIFGAEPWTND 220
                                              ********************************************************************** PP

                                TIGR02155 211 mrkelearlgikaldiyGlseviGpGvanecvetkdGlviwedhfypeiidpetgevlpdGeeGelvftt 280
                                              mr+++e+r+gi+a+diyGlsev+GpGva ecvetkdG++iwedhfypeiidpetgevlpdGe Gelvft+
  lcl|FitnessBrowser__BFirm:BPHYT_RS17360 221 MRQAIEKRMGIDAVDIYGLSEVMGPGVASECVETKDGPTIWEDHFYPEIIDPETGEVLPDGELGELVFTS 290
                                              ********************************************************************** PP

                                TIGR02155 281 ltkealpviryrtrdltrllpgtartmrrmdkikGrsddllilrGvnvfptqleevllkldklsphyqle 350
                                              ltkealp++ryrtrdltrllpg+artmrrm+ki+Grsdd++i+rGvnvfptq+ee+llk+  l+phyq+ 
  lcl|FitnessBrowser__BFirm:BPHYT_RS17360 291 LTKEALPIVRYRTRDLTRLLPGSARTMRRMEKITGRSDDMMIVRGVNVFPTQIEELLLKQRALAPHYQIV 360
                                              ********************************************************************** PP

                                TIGR02155 351 ltreGaldeltlkvelkdesaalrlleqksllakkiekkikaevgvsvdvelvepgslerseGkakrvvd 420
                                              lt+eG ld ltl+ve  +esa  +     s+ ++ +  +ika +gvs+ v++ +   +ers Gka+rvvd
  lcl|FitnessBrowser__BFirm:BPHYT_RS17360 361 LTKEGPLDVLTLNVEPCPESAPDT--AALSTAKQALAYDIKALIGVSAVVNVLAVNGIERSVGKARRVVD 428
                                              *******************99877..445567999*********************************** PP

                                TIGR02155 421 kr 422
                                              kr
  lcl|FitnessBrowser__BFirm:BPHYT_RS17360 429 KR 430
                                              *8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (422 nodes)
Target sequences:                          1  (434 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.44
//
[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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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