Alignments for a candidate for paaK in Jannaschia aquimarina GSW-M26

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaK in Jannaschia aquimarina GSW-M26

Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_043918386.1 jaqu_RS07785 phenylacetate--CoA ligase

Query= BRENDA::B4E7B5
         (432 letters)



>NCBI__GCF_000877395.1:WP_043918386.1
          Length = 436

 Score =  582 bits (1499), Expect = e-170
 Identities = 287/427 (67%), Positives = 348/427 (81%), Gaps = 1/427 (0%)

Query: 4   PLPLEPIETASRDELTALQLERLKWSLRHAYDHSPVYRRKFDEAGVHPDDLKTLADLSRF 63
           P  LEPIETAS DEL ALQL+RL+ SLRHAY++  +YRR+FDEAGVHPDDL+ L+DL+RF
Sbjct: 8   PGDLEPIETASLDELRALQLDRLRRSLRHAYENVDLYRRRFDEAGVHPDDLRELSDLARF 67

Query: 64  PFTTKGDLRDSYPFGMFAVPQDRISRIHASSGTTGKPTVVGYTAADIDTWANLVARSIRA 123
           PFT K DLRD+YPFG+FAVP++RI R+HASSGTTGKPTVVGYT ADI+ W++++ARS+RA
Sbjct: 68  PFTQKSDLRDAYPFGLFAVPRERIVRVHASSGTTGKPTVVGYTKADIEMWSDVMARSLRA 127

Query: 124 AGARRGDKVHVSYGYGLFTGGLGAHYGAERAGLTVIPFGGGQTEKQVQLIQDFRPDIIMV 183
           AG R GD VH +YGYGLFTGGLGAHYG ER G TV+P GGGQTE+Q+ LI DFRP  I+V
Sbjct: 128 AGLRAGDMVHNAYGYGLFTGGLGAHYGIERLGGTVVPMGGGQTERQIALIADFRPKGILV 187

Query: 184 TPSYMLSIADEIERQGLDPVQSSLRIGIFGAEPWTNDMRVAIEQRMGIDAVDIYGLSEVM 243
           TPSYML++ +     G+DP ++SL++G+FGAEPWT+ MR  IE    + AVDIYGLSE++
Sbjct: 188 TPSYMLNVLEAHLAAGIDPRETSLQVGVFGAEPWTDSMRKRIEDAFDMHAVDIYGLSEII 247

Query: 244 GPGVASECVETKDGPTIWEDHFYPEIIDPETGEVLPDGELGELVFTSLTKEALPIIRYRT 303
           GPGVA+ECVETKDG  IWEDHFYPEIIDPETGEVL DGE GELVFT+LT+E +P+IRYRT
Sbjct: 248 GPGVANECVETKDGLHIWEDHFYPEIIDPETGEVLDDGEEGELVFTTLTREGMPMIRYRT 307

Query: 304 RDLTRLLPGTARTMRRMEKITGRSDDMMIVRGVNVFPTQIEEQLLKQRALAPHYQIVLTK 363
           RDLTRL+PGTARTMRRMEKITGRSDDM+I+RGVNVFPTQIEEQ+L    LAPH+QI L  
Sbjct: 308 RDLTRLMPGTARTMRRMEKITGRSDDMIILRGVNVFPTQIEEQVLATPGLAPHFQIELVS 367

Query: 364 EGPLDVLTLNVEPCPETAPDTAAIQVAKQALAYDIKSLIGVTAVINVLPVNGIERSVGKA 423
           +GP+  + + VE  P  A D  +   A+  LA  IK+++GVTA + V   + + RS GKA
Sbjct: 368 DGPMASMRVLVEASPNEA-DAPSRAAAQAELANRIKTMVGVTAEVQVGGPDSVARSQGKA 426

Query: 424 RRVVDKR 430
            RVVD+R
Sbjct: 427 IRVVDRR 433


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: 646
Number of extensions: 12
Number of successful extensions: 2
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: 436
Length adjustment: 32
Effective length of query: 400
Effective length of database: 404
Effective search space:   161600
Effective search space used:   161600
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 WP_043918386.1 jaqu_RS07785 (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.1973317.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.2e-213  693.4   0.0   4.8e-213  693.2   0.0    1.0  1  NCBI__GCF_000877395.1:WP_043918386.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000877395.1:WP_043918386.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  693.2   0.0  4.8e-213  4.8e-213       1     422 []      15     433 ..      15     433 .. 0.99

  Alignments for each domain:
  == domain 1  score: 693.2 bits;  conditional E-value: 4.8e-213
                             TIGR02155   1 eklsldelralqlerlkvsvkrayenvpayrkafdaagvkpddlkelsdlakfpltaksdlrdnypfdllavp 73 
                                           e++sldelralql+rl+ s+++ayenv  yr++fd+agv+pddl+elsdla+fp+t+ksdlrd ypf+l+avp
  NCBI__GCF_000877395.1:WP_043918386.1  15 ETASLDELRALQLDRLRRSLRHAYENVDLYRRRFDEAGVHPDDLRELSDLARFPFTQKSDLRDAYPFGLFAVP 87 
                                           89*********************************************************************** PP

                             TIGR02155  74 rekvvrvhassGttGkptvvaytqkdldtwsevvarslraaGGrkgdllhnayGyGlftGGlGvhyGaeklGa 146
                                           re++vrvhassGttGkptvv+yt+ d+++ws+v+arslraaG r+gd++hnayGyGlftGGlG+hyG e+lG 
  NCBI__GCF_000877395.1:WP_043918386.1  88 RERIVRVHASSGTTGKPTVVGYTKADIEMWSDVMARSLRAAGLRAGDMVHNAYGYGLFTGGLGAHYGIERLGG 160
                                           ************************************************************************* PP

                             TIGR02155 147 tvvpisGGqtekqvqliqdfkpdiiavtpsyilalleelkrlgidpedislkvailGaepwteamrkelearl 219
                                           tvvp+ GGqte+q+ li df+p+ i vtpsy+l++le+    gidp+++sl+v+++Gaepwt+ mrk +e+++
  NCBI__GCF_000877395.1:WP_043918386.1 161 TVVPMGGGQTERQIALIADFRPKGILVTPSYMLNVLEAHLAAGIDPRETSLQVGVFGAEPWTDSMRKRIEDAF 233
                                           ************************************************************************* PP

                             TIGR02155 220 gikaldiyGlseviGpGvanecvetkdGlviwedhfypeiidpetgevlpdGeeGelvfttltkealpviryr 292
                                           +++a+diyGlse+iGpGvanecvetkdGl+iwedhfypeiidpetgevl dGeeGelvfttlt+e++p+iryr
  NCBI__GCF_000877395.1:WP_043918386.1 234 DMHAVDIYGLSEIIGPGVANECVETKDGLHIWEDHFYPEIIDPETGEVLDDGEEGELVFTTLTREGMPMIRYR 306
                                           ************************************************************************* PP

                             TIGR02155 293 trdltrllpgtartmrrmdkikGrsddllilrGvnvfptqleevllkldklsphyqleltreGaldeltlkve 365
                                           trdltrl+pgtartmrrm+ki+Grsdd++ilrGvnvfptq+ee +l+++ l+ph+q+el+ +G + ++ + ve
  NCBI__GCF_000877395.1:WP_043918386.1 307 TRDLTRLMPGTARTMRRMEKITGRSDDMIILRGVNVFPTQIEEQVLATPGLAPHFQIELVSDGPMASMRVLVE 379
                                           ************************************************************************* PP

                             TIGR02155 366 lkdesaalrlleqksllakkiekkikaevgvsvdvelvepgslerseGkakrvvdkr 422
                                           + ++ a++    ++++ + ++ ++ik++vgv+++v++  p s+ rs+Gka rvvd+r
  NCBI__GCF_000877395.1:WP_043918386.1 380 ASPNEADAP---SRAAAQAELANRIKTMVGVTAEVQVGGPDSVARSQGKAIRVVDRR 433
                                           **9887765...5667789************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (422 nodes)
Target sequences:                          1  (436 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 16.81
//
[ok]

This GapMind analysis is from Sep 24 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:

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 2024 update 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