Alignments for a candidate for paaK in Bradyrhizobium sp. BTAi1

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaK in Bradyrhizobium sp. BTAi1

Align Phenylacetate-coenzyme A ligase; Phenylacetyl-CoA ligase; PA-CoA ligase; EC 6.2.1.30 (characterized)
to candidate WP_012043018.1 BBTA_RS13375 phenylacetate--CoA ligase

Query= SwissProt::Q9L9C1
         (440 letters)



>NCBI__GCF_000015165.1:WP_012043018.1
          Length = 442

 Score =  578 bits (1490), Expect = e-169
 Identities = 284/434 (65%), Positives = 340/434 (78%), Gaps = 13/434 (2%)

Query: 10  DLEPIEKASQDELRALQLERLKWSVRHAYENVPHYRKAFDAKGVHPDDLKSLADLAKFPF 69
           D++  E+AS+DE+ ALQ +RL WS++HAY+NV HYR+AFD  GVHP D + LADLAKFPF
Sbjct: 15  DMDATERASRDEIMALQTKRLAWSLKHAYDNVAHYRRAFDTAGVHPSDFRELADLAKFPF 74

Query: 70  TAKGDLRDNYPFGMFAVPREKVARVHASSGTTGKPTVVGYTLKDIDTWATVVARSIRASG 129
           T K DLRDNYPF MFAVPRE++ RVHASSGTTGKP VVGYT  DI TW+ V+ARSIRA+G
Sbjct: 75  TVKTDLRDNYPFNMFAVPREQLVRVHASSGTTGKPIVVGYTRNDIATWSHVMARSIRAAG 134

Query: 130 GRAGDMVHIAYGYGLFTGGLGAHYGAEKLGCTVVPMSGGQTEKQIQLIQDFKPDIIMVTP 189
           GR+G ++H AYGYGLFTGGLG HYGAE+LGCTVVP+SGG TE+Q+QLI DF+PDII VTP
Sbjct: 135 GRSGMIIHNAYGYGLFTGGLGVHYGAEELGCTVVPISGGMTERQVQLINDFRPDIITVTP 194

Query: 190 SYMLTVLDEMERMGIDPHQTSLKVGIFGAEPWTQAMRAAMEARAGIDAVDIYGLSEVMGP 249
           SYML +LDE +R G+DP Q+SLK+GIFGAEPWT AMRA +E    +DA DIYGLSEV+GP
Sbjct: 195 SYMLAILDEFKRQGLDPRQSSLKIGIFGAEPWTNAMRAEIEDAFAMDATDIYGLSEVIGP 254

Query: 250 GVANECIEAKDGPVIWEDHFYPEIIDPHTGEVLPDGSEGELVFTTLTKEAMPVIRYRTRD 309
           GVA EC+E KDG  IWEDHFYPEI+DP TG+VLPDG  GELVFT+LTKEA PVIRYRTRD
Sbjct: 255 GVAQECLETKDGLHIWEDHFYPEIVDPDTGKVLPDGEMGELVFTSLTKEAFPVIRYRTRD 314

Query: 310 LTRLLPPTAR-SMRRMAKITGRSDDMLIIRGVNLFPTQVEELICKNPKLAPQYLLEVDKD 368
           LTRLLP TAR  MRRM K+TGRSDDM+I+RGVNLFP+Q+EE++         ++LE+ ++
Sbjct: 315 LTRLLPGTARPGMRRMEKVTGRSDDMIILRGVNLFPSQIEEILLTTEWCGGHFMLELTRE 374

Query: 369 GHMDTLTVKVEINP----EANVGRHPEQKEALAKELQHDIKTFIGVSAKVHVCEPFAIER 424
           G MD LT+  E  P    E  +G H       A+ +   IK  IGV+AKV    P  +ER
Sbjct: 375 GRMDELTIYAESRPEHWDETGLGAH-------AERISIHIKNTIGVTAKVKAVPPDTLER 427

Query: 425 VTIGKAKRVVDRRP 438
            + GKAKR+ DRRP
Sbjct: 428 -SAGKAKRIKDRRP 440


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: 700
Number of extensions: 18
Number of successful extensions: 4
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: 442
Length adjustment: 32
Effective length of query: 408
Effective length of database: 410
Effective search space:   167280
Effective search space used:   167280
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_012043018.1 BBTA_RS13375 (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.28462.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.9e-230  749.5   0.0   4.5e-230  749.3   0.0    1.0  1  lcl|NCBI__GCF_000015165.1:WP_012043018.1  BBTA_RS13375 phenylacetate--CoA 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000015165.1:WP_012043018.1  BBTA_RS13375 phenylacetate--CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  749.3   0.0  4.5e-230  4.5e-230       1     422 []      20     439 ..      20     439 .. 0.99

  Alignments for each domain:
  == domain 1  score: 749.3 bits;  conditional E-value: 4.5e-230
                                 TIGR02155   1 eklsldelralqlerlkvsvkrayenvpayrkafdaagvkpddlkelsdlakfpltaksdlrdnypfdl 69 
                                               e++s+de++alq++rl +s+k+ay+nv++yr+afd agv+p+d++el+dlakfp+t+k+dlrdnypf++
  lcl|NCBI__GCF_000015165.1:WP_012043018.1  20 ERASRDEIMALQTKRLAWSLKHAYDNVAHYRRAFDTAGVHPSDFRELADLAKFPFTVKTDLRDNYPFNM 88 
                                               799****************************************************************** PP

                                 TIGR02155  70 lavprekvvrvhassGttGkptvvaytqkdldtwsevvarslraaGGrkgdllhnayGyGlftGGlGvh 138
                                               +avpre++vrvhassGttGkp+vv+yt++d+ tws+v+ars+raaGGr+g+++hnayGyGlftGGlGvh
  lcl|NCBI__GCF_000015165.1:WP_012043018.1  89 FAVPREQLVRVHASSGTTGKPIVVGYTRNDIATWSHVMARSIRAAGGRSGMIIHNAYGYGLFTGGLGVH 157
                                               ********************************************************************* PP

                                 TIGR02155 139 yGaeklGatvvpisGGqtekqvqliqdfkpdiiavtpsyilalleelkrlgidpedislkvailGaepw 207
                                               yGae lG+tvvpisGG+te+qvqli+df+pdii+vtpsy+la+l+e+kr+g+dp++ slk++i+Gaepw
  lcl|NCBI__GCF_000015165.1:WP_012043018.1 158 YGAEELGCTVVPISGGMTERQVQLINDFRPDIITVTPSYMLAILDEFKRQGLDPRQSSLKIGIFGAEPW 226
                                               ********************************************************************* PP

                                 TIGR02155 208 teamrkelearlgikaldiyGlseviGpGvanecvetkdGlviwedhfypeiidpetgevlpdGeeGel 276
                                               t+amr+e+e+++ ++a+diyGlseviGpGva+ec+etkdGl+iwedhfypei+dp+tg+vlpdGe Gel
  lcl|NCBI__GCF_000015165.1:WP_012043018.1 227 TNAMRAEIEDAFAMDATDIYGLSEVIGPGVAQECLETKDGLHIWEDHFYPEIVDPDTGKVLPDGEMGEL 295
                                               ********************************************************************* PP

                                 TIGR02155 277 vfttltkealpviryrtrdltrllpgtart.mrrmdkikGrsddllilrGvnvfptqleevllkldkls 344
                                               vft+ltkea+pviryrtrdltrllpgtar+ mrrm+k++Grsdd++ilrGvn+fp+q+ee+ll++++++
  lcl|NCBI__GCF_000015165.1:WP_012043018.1 296 VFTSLTKEAFPVIRYRTRDLTRLLPGTARPgMRRMEKVTGRSDDMIILRGVNLFPSQIEEILLTTEWCG 364
                                               *****************************99************************************** PP

                                 TIGR02155 345 phyqleltreGaldeltlkvelkdesaalrlleqksllakkiekkikaevgvsvdvelvepgslerseG 413
                                               +h++leltreG++delt+ +e ++e ++ + l  +   a++i+ +ik+++gv+++v+ v p +lers G
  lcl|NCBI__GCF_000015165.1:WP_012043018.1 365 GHFMLELTREGRMDELTIYAESRPEHWDETGLGAH---AERISIHIKNTIGVTAKVKAVPPDTLERSAG 430
                                               ****************************9988777...9****************************** PP

                                 TIGR02155 414 kakrvvdkr 422
                                               kakr+ d+r
  lcl|NCBI__GCF_000015165.1:WP_012043018.1 431 KAKRIKDRR 439
                                               *******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (422 nodes)
Target sequences:                          1  (442 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.59
//
[ok]

This GapMind analysis is from Sep 24 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