Alignments for a candidate for paaK in Rhodopseudomonas palustris CGA009

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaK in Rhodopseudomonas palustris CGA009

Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_011157450.1 TX73_RS08795 phenylacetate--CoA ligase

Query= BRENDA::B4E7B5
         (432 letters)



>NCBI__GCF_000195775.1:WP_011157450.1
          Length = 443

 Score =  580 bits (1495), Expect = e-170
 Identities = 289/425 (68%), Positives = 338/425 (79%), Gaps = 2/425 (0%)

Query: 7   LEPIETASRDELTALQLERLKWSLRHAYDHSPVYRRKFDEAGVHPDDLKTLADLSRFPFT 66
           L+  E ASRDE+ ALQ +RL WSL+HAYD+   Y+  FD  GVHP D + L+DLS+FPFT
Sbjct: 17  LDDAERASRDEIVALQTKRLAWSLKHAYDNVAHYKAAFDRKGVHPSDFRQLSDLSKFPFT 76

Query: 67  TKGDLRDSYPFGMFAVPQDRISRIHASSGTTGKPTVVGYTAADIDTWANLVARSIRAAGA 126
            K DLRD+YPF MFAVP++ + R+HASSGTTGKP VVGYT  DIDTWA ++ARS+RAAGA
Sbjct: 77  VKTDLRDNYPFAMFAVPRESLVRVHASSGTTGKPIVVGYTPKDIDTWATVMARSLRAAGA 136

Query: 127 RRGDKVHVSYGYGLFTGGLGAHYGAERAGLTVIPFGGGQTEKQVQLIQDFRPDIIMVTPS 186
           RRG  +H SYGYGLFTGGLGAHYG E+ G TV+P  GG TE+QVQLI DFRPDII VTPS
Sbjct: 137 RRGMIIHNSYGYGLFTGGLGAHYGGEKLGCTVVPVSGGMTERQVQLINDFRPDIITVTPS 196

Query: 187 YMLSIADEIERQGLDPVQSSLRIGIFGAEPWTNDMRVAIEQRMGIDAVDIYGLSEVMGPG 246
           YML+I DE +RQGLDP QSSL+ G+FGAEPWTN MR  IEQ   +DA DIYGLSEV+GPG
Sbjct: 197 YMLAILDEFKRQGLDPRQSSLKYGVFGAEPWTNAMRAEIEQAFDMDATDIYGLSEVIGPG 256

Query: 247 VASECVETKDGPTIWEDHFYPEIIDPETGEVLPDGELGELVFTSLTKEALPIIRYRTRDL 306
           VA ECVETKDG  IWEDHFYPE+IDP+TG+VLPDGE GELVFTSLTKEA P+IRYRTRDL
Sbjct: 257 VAQECVETKDGLHIWEDHFYPEVIDPDTGDVLPDGEKGELVFTSLTKEAFPVIRYRTRDL 316

Query: 307 TRLLPGTART-MRRMEKITGRSDDMMIVRGVNVFPTQIEEQLLKQRALAPHYQIVLTKEG 365
           TRLLPGTAR  MRRMEKITGRSDDM+I+RGVNVFPTQIEE LL       H+ I LT+EG
Sbjct: 317 TRLLPGTARPGMRRMEKITGRSDDMIILRGVNVFPTQIEEVLLGTDWCGGHFIIELTREG 376

Query: 366 PLDVLTLNVEPCPETAPDTAAIQVAKQALAYDIKSLIGVTAVINVLPVNGIERSVGKARR 425
            +D +T+  E  PE+      +  A++A AY IK+ IG++  I V+P + +ERS+GKARR
Sbjct: 377 RMDEMTVLAEARPESWDGAGLVPHAERAAAY-IKNTIGISTTIKVVPPDTLERSLGKARR 435

Query: 426 VVDKR 430
           V DKR
Sbjct: 436 VFDKR 440


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: 653
Number of extensions: 20
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: 432
Length of database: 443
Length adjustment: 32
Effective length of query: 400
Effective length of database: 411
Effective search space:   164400
Effective search space used:   164400
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_011157450.1 TX73_RS08795 (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.4286.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.2e-228  742.3   0.0     7e-228  742.1   0.0    1.0  1  lcl|NCBI__GCF_000195775.1:WP_011157450.1  TX73_RS08795 phenylacetate--CoA 


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000195775.1:WP_011157450.1  TX73_RS08795 phenylacetate--CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  742.1   0.0    7e-228    7e-228       1     422 []      21     440 ..      21     440 .. 0.99

  Alignments for each domain:
  == domain 1  score: 742.1 bits;  conditional E-value: 7e-228
                                 TIGR02155   1 eklsldelralqlerlkvsvkrayenvpayrkafdaagvkpddlkelsdlakfpltaksdlrdnypfdl 69 
                                               e++s+de+ alq++rl +s+k+ay+nv++y++afd++gv+p+d+++lsdl kfp+t+k+dlrdnypf +
  lcl|NCBI__GCF_000195775.1:WP_011157450.1  21 ERASRDEIVALQTKRLAWSLKHAYDNVAHYKAAFDRKGVHPSDFRQLSDLSKFPFTVKTDLRDNYPFAM 89 
                                               799****************************************************************** PP

                                 TIGR02155  70 lavprekvvrvhassGttGkptvvaytqkdldtwsevvarslraaGGrkgdllhnayGyGlftGGlGvh 138
                                               +avpre +vrvhassGttGkp+vv+yt kd+dtw++v+arslraaG r+g+++hn+yGyGlftGGlG+h
  lcl|NCBI__GCF_000195775.1:WP_011157450.1  90 FAVPRESLVRVHASSGTTGKPIVVGYTPKDIDTWATVMARSLRAAGARRGMIIHNSYGYGLFTGGLGAH 158
                                               ********************************************************************* PP

                                 TIGR02155 139 yGaeklGatvvpisGGqtekqvqliqdfkpdiiavtpsyilalleelkrlgidpedislkvailGaepw 207
                                               yG eklG+tvvp+sGG+te+qvqli+df+pdii+vtpsy+la+l+e+kr+g+dp++ slk++++Gaepw
  lcl|NCBI__GCF_000195775.1:WP_011157450.1 159 YGGEKLGCTVVPVSGGMTERQVQLINDFRPDIITVTPSYMLAILDEFKRQGLDPRQSSLKYGVFGAEPW 227
                                               ********************************************************************* PP

                                 TIGR02155 208 teamrkelearlgikaldiyGlseviGpGvanecvetkdGlviwedhfypeiidpetgevlpdGeeGel 276
                                               t+amr+e+e++++++a+diyGlseviGpGva+ecvetkdGl+iwedhfype+idp+tg+vlpdGe+Gel
  lcl|NCBI__GCF_000195775.1:WP_011157450.1 228 TNAMRAEIEQAFDMDATDIYGLSEVIGPGVAQECVETKDGLHIWEDHFYPEVIDPDTGDVLPDGEKGEL 296
                                               ********************************************************************* PP

                                 TIGR02155 277 vfttltkealpviryrtrdltrllpgtart.mrrmdkikGrsddllilrGvnvfptqleevllkldkls 344
                                               vft+ltkea+pviryrtrdltrllpgtar+ mrrm+ki+Grsdd++ilrGvnvfptq+eevll++d+++
  lcl|NCBI__GCF_000195775.1:WP_011157450.1 297 VFTSLTKEAFPVIRYRTRDLTRLLPGTARPgMRRMEKITGRSDDMIILRGVNVFPTQIEEVLLGTDWCG 365
                                               *****************************99************************************** PP

                                 TIGR02155 345 phyqleltreGaldeltlkvelkdesaalrlleqksllakkiekkikaevgvsvdvelvepgslerseG 413
                                               +h+++eltreG++de+t+ +e+++es+++  l+ +   a++    ik+++g+s+ +++v p +lers G
  lcl|NCBI__GCF_000195775.1:WP_011157450.1 366 GHFIIELTREGRMDEMTVLAEARPESWDGAGLVPH---AERAAAYIKNTIGISTTIKVVPPDTLERSLG 431
                                               ******************************99888...899999************************* PP

                                 TIGR02155 414 kakrvvdkr 422
                                               ka+rv+dkr
  lcl|NCBI__GCF_000195775.1:WP_011157450.1 432 KARRVFDKR 440
                                               ********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (422 nodes)
Target sequences:                          1  (443 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: 00:00:00.02
# Mc/sec: 7.65
//
[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 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