Alignments for a candidate for paaK in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaK in Cupriavidus basilensis 4G11

Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate RR42_RS18265 RR42_RS18265 phenylacetate--CoA ligase

Query= BRENDA::B4E7B5
         (432 letters)



>FitnessBrowser__Cup4G11:RR42_RS18265
          Length = 433

 Score =  690 bits (1780), Expect = 0.0
 Identities = 339/429 (79%), Positives = 378/429 (88%), Gaps = 3/429 (0%)

Query: 3   TPLPLEPIETASRDELTALQLERLKWSLRHAYDHSPVYRRKFDEAGVHPDDLKTLADLSR 62
           T LPLEPIETASRD L ALQLERL+WSL HAY +SPVYRRKFD AGVHP+ ++TLADL+R
Sbjct: 5   TDLPLEPIETASRDALQALQLERLQWSLNHAYQNSPVYRRKFDAAGVHPNQIRTLADLAR 64

Query: 63  FPFTTKGDLRDSYPFGMFAVPQDRISRIHASSGTTGKPTVVGYTAADIDTWANLVARSIR 122
           FPFTTK DLRDSYPFGMFAVPQDR++RIHASSGTTGKPTVVGYT  DIDTWA +VARSIR
Sbjct: 65  FPFTTKQDLRDSYPFGMFAVPQDRVARIHASSGTTGKPTVVGYTLKDIDTWATVVARSIR 124

Query: 123 AAGARRGDKVHVSYGYGLFTGGLGAHYGAERAGLTVIPFGGGQTEKQVQLIQDFRPDIIM 182
           AAGARRGDKVH+SYGYGLFTGGLGAHYG E+AGLT IPFGGGQTE+QVQLIQDF+P++IM
Sbjct: 125 AAGARRGDKVHISYGYGLFTGGLGAHYGVEKAGLTAIPFGGGQTERQVQLIQDFKPEVIM 184

Query: 183 VTPSYMLSIADEIERQGLDPVQSSLRIGIFGAEPWTNDMRVAIEQRMGIDAVDIYGLSEV 242
           VTPSYML+IADE ERQG+DP  SSL++GIFGAEPWT +MR+AIE+RMGI AVDIYGLSEV
Sbjct: 185 VTPSYMLAIADEFERQGIDPTASSLKVGIFGAEPWTPEMRLAIEKRMGISAVDIYGLSEV 244

Query: 243 MGPGVASECVETKDGPTIWEDHFYPEIIDPETGEVLPDGELGELVFTSLTKEALPIIRYR 302
           MGPGVASEC +TKDGPTIWEDHFYPE+IDP TGEVLPDGE GELVFTSL+KEALPI+RYR
Sbjct: 245 MGPGVASECAQTKDGPTIWEDHFYPEVIDPLTGEVLPDGEFGELVFTSLSKEALPIVRYR 304

Query: 303 TRDLTRLLPGTAR-TMRRMEKITGRSDDMMIVRGVNVFPTQIEEQLLKQRALAPHYQIVL 361
           TRDLTRLLPG+AR   RRMEK+TGR+DDMMI+RGVNVFP+QIEE +LK   LAPHYQ VL
Sbjct: 305 TRDLTRLLPGSARGAFRRMEKVTGRTDDMMIIRGVNVFPSQIEELILKHAELAPHYQCVL 364

Query: 362 TKEGPLDVLTLNVEPCPETAPDTAAIQVAKQALAYDIKSLIGVTAVINVLPVNGIERSVG 421
           TK+G LDVLT+ VE C     D AA   A   L YDIK+ IGVT  I +LP  G+ERSVG
Sbjct: 365 TKDGHLDVLTVRVE-CAH-GVDPAATHQASAQLTYDIKAFIGVTVGIEILPSGGVERSVG 422

Query: 422 KARRVVDKR 430
           KARR+VD+R
Sbjct: 423 KARRIVDQR 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: 721
Number of extensions: 18
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: 433
Length adjustment: 32
Effective length of query: 400
Effective length of database: 401
Effective search space:   160400
Effective search space used:   160400
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 RR42_RS18265 RR42_RS18265 (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.20623.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   4.1e-210  683.6   0.0   4.7e-210  683.4   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS18265  RR42_RS18265 phenylacetate--CoA 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS18265  RR42_RS18265 phenylacetate--CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  683.4   0.0  4.7e-210  4.7e-210       1     422 []      13     431 ..      13     431 .. 0.98

  Alignments for each domain:
  == domain 1  score: 683.4 bits;  conditional E-value: 4.7e-210
                                 TIGR02155   1 eklsldelralqlerlkvsvkrayenvpayrkafdaagvkpddlkelsdlakfpltaksdlrdnypfdl 69 
                                               e++s+d l+alqlerl++s+++ay+n p+yr++fdaagv+p+ +++l+dla+fp+t+k+dlrd ypf++
  lcl|FitnessBrowser__Cup4G11:RR42_RS18265  13 ETASRDALQALQLERLQWSLNHAYQNSPVYRRKFDAAGVHPNQIRTLADLARFPFTTKQDLRDSYPFGM 81 
                                               899****************************************************************** PP

                                 TIGR02155  70 lavprekvvrvhassGttGkptvvaytqkdldtwsevvarslraaGGrkgdllhnayGyGlftGGlGvh 138
                                               +avp+++v+r+hassGttGkptvv+yt kd+dtw++vvars+raaG r+gd++h++yGyGlftGGlG+h
  lcl|FitnessBrowser__Cup4G11:RR42_RS18265  82 FAVPQDRVARIHASSGTTGKPTVVGYTLKDIDTWATVVARSIRAAGARRGDKVHISYGYGLFTGGLGAH 150
                                               ********************************************************************* PP

                                 TIGR02155 139 yGaeklGatvvpisGGqtekqvqliqdfkpdiiavtpsyilalleelkrlgidpedislkvailGaepw 207
                                               yG ek G t +p+ GGqte+qvqliqdfkp++i+vtpsy+la+++e++r+gidp+  slkv+i+Gaepw
  lcl|FitnessBrowser__Cup4G11:RR42_RS18265 151 YGVEKAGLTAIPFGGGQTERQVQLIQDFKPEVIMVTPSYMLAIADEFERQGIDPTASSLKVGIFGAEPW 219
                                               ********************************************************************* PP

                                 TIGR02155 208 teamrkelearlgikaldiyGlseviGpGvanecvetkdGlviwedhfypeiidpetgevlpdGeeGel 276
                                               t +mr ++e+r+gi+a+diyGlsev+GpGva ec +tkdG++iwedhfype+idp tgevlpdGe Gel
  lcl|FitnessBrowser__Cup4G11:RR42_RS18265 220 TPEMRLAIEKRMGISAVDIYGLSEVMGPGVASECAQTKDGPTIWEDHFYPEVIDPLTGEVLPDGEFGEL 288
                                               ********************************************************************* PP

                                 TIGR02155 277 vfttltkealpviryrtrdltrllpgtart.mrrmdkikGrsddllilrGvnvfptqleevllkldkls 344
                                               vft+l+kealp++ryrtrdltrllpg+ar   rrm+k++Gr+dd++i+rGvnvfp+q+ee++lk  +l+
  lcl|FitnessBrowser__Cup4G11:RR42_RS18265 289 VFTSLSKEALPIVRYRTRDLTRLLPGSARGaFRRMEKVTGRTDDMMIIRGVNVFPSQIEELILKHAELA 357
                                               *****************************879************************************* PP

                                 TIGR02155 345 phyqleltreGaldeltlkvelkdesaalrlleqksllakkiekkikaevgvsvdvelvepgslerseG 413
                                               phyq  lt++G+ld lt++ve  +    + ++    + + ++  +ika++gv+v +e+  +g +ers G
  lcl|FitnessBrowser__Cup4G11:RR42_RS18265 358 PHYQCVLTKDGHLDVLTVRVECAHGVDPAATH----QASAQLTYDIKAFIGVTVGIEILPSGGVERSVG 422
                                               *********************99666555544....4468999************************** PP

                                 TIGR02155 414 kakrvvdkr 422
                                               ka+r+vd+r
  lcl|FitnessBrowser__Cup4G11:RR42_RS18265 423 KARRIVDQR 431
                                               *******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (422 nodes)
Target sequences:                          1  (433 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: 10.53
//
[ok]

This GapMind analysis is from Sep 17 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