Alignments for a candidate for paaK in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaK in Phaeobacter inhibens BS107

Align Phenylacetate-coenzyme A ligase; Phenylacetyl-CoA ligase; PA-CoA ligase; EC 6.2.1.30 (characterized)
to candidate GFF2640 PGA1_c26800 phenylacetate-CoA ligase PaaK

Query= SwissProt::Q9L9C1
         (440 letters)



>FitnessBrowser__Phaeo:GFF2640
          Length = 436

 Score =  604 bits (1557), Expect = e-177
 Identities = 299/436 (68%), Positives = 350/436 (80%), Gaps = 4/436 (0%)

Query: 5   TPSPGDLEPIEKASQDELRALQLERLKWSVRHAYENVPHYRKAFDAKGVHPDDLKSLADL 64
           +P  G+L+PIE AS DE+R+LQL+RLKWS+RHAY+NV  Y++ FD  GVHPDDL+ L+DL
Sbjct: 5   SPKKGELDPIEIASIDEIRSLQLDRLKWSLRHAYDNVAMYKQRFDEAGVHPDDLQQLSDL 64

Query: 65  AKFPFTAKGDLRDNYPFGMFAVPREKVARVHASSGTTGKPTVVGYTLKDIDTWATVVARS 124
           AKFPFT K DLRDNYPFG+FAVPRE++ R+HASSGTTGKPTVVGYT  DI  WA +VARS
Sbjct: 65  AKFPFTYKNDLRDNYPFGLFAVPREQIMRLHASSGTTGKPTVVGYTANDISNWADLVARS 124

Query: 125 IRASGGRAGDMVHIAYGYGLFTGGLGAHYGAEKLGCTVVPMSGGQTEKQIQLIQDFKPDI 184
           +RASG R GDMVH AYGYGLFTGGLGAHYG E+LG TVVPMSGGQTEKQ+ LI DFKPD 
Sbjct: 125 LRASGLRKGDMVHNAYGYGLFTGGLGAHYGIERLGATVVPMSGGQTEKQVGLITDFKPDG 184

Query: 185 IMVTPSYMLTVLDEMERMGIDPHQTSLKVGIFGAEPWTQAMRAAMEARAGIDAVDIYGLS 244
           IMVTPSYML +L++  ++G+DP + SLKVG+FGAEPWT AMR  +E    + AVDIYGLS
Sbjct: 185 IMVTPSYMLNILEQYHKVGMDPRECSLKVGVFGAEPWTDAMRREVEQAFDMHAVDIYGLS 244

Query: 245 EVMGPGVANECIEAKDGPVIWEDHFYPEIIDPHTGEVLPDGSEGELVFTTLTKEAMPVIR 304
           E+MGPGVANEC+E KDGPVIWEDHF PEIIDP TGEVLPDG  GELVFTTLTKE +P++R
Sbjct: 245 EIMGPGVANECVETKDGPVIWEDHFLPEIIDPQTGEVLPDGEMGELVFTTLTKEGLPMVR 304

Query: 305 YRTRDLTRLLPPTARSMRRMAKITGRSDDMLIIRGVNLFPTQVEELICKNPKLAPQYLLE 364
           YRTRDLTRLLP TARSMRRM KITGRSDDM+I+RGVN+FP+QVEE +     LAP Y +E
Sbjct: 305 YRTRDLTRLLPGTARSMRRMEKITGRSDDMIILRGVNVFPSQVEEQLLATGGLAPYYQIE 364

Query: 365 VDKDGHMDTLTVKVEINPEANVGRHPEQKEALAKELQHDIKTFIGVSAKVHVCEPFAIER 424
           + K G MD + V VE NP+A        K A A+ L   IK  +GVS ++ V EP ++ER
Sbjct: 365 LYKSGRMDAMRVFVEANPDAT---DELSKTAAARMLTKRIKDMVGVSTEIIVGEPGSVER 421

Query: 425 VTIGKAKRVVDRRPKE 440
            + GKAKRVVD R KE
Sbjct: 422 -SQGKAKRVVDNRSKE 436


Lambda     K      H
   0.318    0.137    0.406 

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: 668
Number of extensions: 16
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: 440
Length of database: 436
Length adjustment: 32
Effective length of query: 408
Effective length of database: 404
Effective search space:   164832
Effective search space used:   164832
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 GFF2640 PGA1_c26800 (phenylacetate-CoA ligase PaaK)
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.6807.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   1.8e-219  714.4   0.0     2e-219  714.3   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF2640  PGA1_c26800 phenylacetate-CoA li


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF2640  PGA1_c26800 phenylacetate-CoA ligase PaaK
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  714.3   0.0    2e-219    2e-219       1     422 []      15     433 ..      15     433 .. 0.99

  Alignments for each domain:
  == domain 1  score: 714.3 bits;  conditional E-value: 2e-219
                          TIGR02155   1 eklsldelralqlerlkvsvkrayenvpayrkafdaagvkpddlkelsdlakfpltaksdlrdnypfdllavprek 76 
                                        e +s de+r+lql+rlk+s+++ay+nv++y+++fd+agv+pddl++lsdlakfp+t k+dlrdnypf+l+avpre+
  lcl|FitnessBrowser__Phaeo:GFF2640  15 EIASIDEIRSLQLDRLKWSLRHAYDNVAMYKQRFDEAGVHPDDLQQLSDLAKFPFTYKNDLRDNYPFGLFAVPREQ 90 
                                        6799************************************************************************ PP

                          TIGR02155  77 vvrvhassGttGkptvvaytqkdldtwsevvarslraaGGrkgdllhnayGyGlftGGlGvhyGaeklGatvvpis 152
                                        ++r+hassGttGkptvv+yt++d+ +w+++varslra+G rkgd++hnayGyGlftGGlG+hyG e+lGatvvp+s
  lcl|FitnessBrowser__Phaeo:GFF2640  91 IMRLHASSGTTGKPTVVGYTANDISNWADLVARSLRASGLRKGDMVHNAYGYGLFTGGLGAHYGIERLGATVVPMS 166
                                        **************************************************************************** PP

                          TIGR02155 153 GGqtekqvqliqdfkpdiiavtpsyilalleelkrlgidpedislkvailGaepwteamrkelearlgikaldiyG 228
                                        GGqtekqv li dfkpd i+vtpsy+l++le+ +++g+dp+++slkv+++Gaepwt+amr+e+e++++++a+diyG
  lcl|FitnessBrowser__Phaeo:GFF2640 167 GGQTEKQVGLITDFKPDGIMVTPSYMLNILEQYHKVGMDPRECSLKVGVFGAEPWTDAMRREVEQAFDMHAVDIYG 242
                                        **************************************************************************** PP

                          TIGR02155 229 lseviGpGvanecvetkdGlviwedhfypeiidpetgevlpdGeeGelvfttltkealpviryrtrdltrllpgta 304
                                        lse++GpGvanecvetkdG+viwedhf peiidp+tgevlpdGe Gelvfttltke+lp++ryrtrdltrllpgta
  lcl|FitnessBrowser__Phaeo:GFF2640 243 LSEIMGPGVANECVETKDGPVIWEDHFLPEIIDPQTGEVLPDGEMGELVFTTLTKEGLPMVRYRTRDLTRLLPGTA 318
                                        **************************************************************************** PP

                          TIGR02155 305 rtmrrmdkikGrsddllilrGvnvfptqleevllkldklsphyqleltreGaldeltlkvelkdesaalrlleqks 380
                                        r+mrrm+ki+Grsdd++ilrGvnvfp+q+ee ll+++ l+p yq+el ++G++d + + ve+++++++     +k+
  lcl|FitnessBrowser__Phaeo:GFF2640 319 RSMRRMEKITGRSDDMIILRGVNVFPSQVEEQLLATGGLAPYYQIELYKSGRMDAMRVFVEANPDATDEL---SKT 391
                                        ***************************************************************9998877...455 PP

                          TIGR02155 381 llakkiekkikaevgvsvdvelvepgslerseGkakrvvdkr 422
                                        + a+ + k+ik++vgvs+++ + epgs+ers+Gkakrvvd+r
  lcl|FitnessBrowser__Phaeo:GFF2640 392 AAARMLTKRIKDMVGVSTEIIVGEPGSVERSQGKAKRVVDNR 433
                                        66999***********************************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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.07
//
[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:

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