Alignments for a candidate for paaK in Nocardiopsis lucentensis DSM 44048

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaK in Nocardiopsis lucentensis DSM 44048

Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_017600844.1 D471_RS0123270 phenylacetate--CoA ligase

Query= BRENDA::B4E7B5
         (432 letters)



>NCBI__GCF_000341125.1:WP_017600844.1
          Length = 451

 Score =  598 bits (1543), Expect = e-176
 Identities = 297/427 (69%), Positives = 341/427 (79%), Gaps = 2/427 (0%)

Query: 4   PLPLEPIETASRDELTALQLERLKWSLRHAYDHSPVYRRKFDEAGVHPDDLKTLADLSRF 63
           P  L+P E    DEL ALQLERL+WSL HAY + P Y+R FDEAGVHP DLK LADL  F
Sbjct: 25  PELLDPAERMGVDELRALQLERLRWSLEHAYTNVPFYKRTFDEAGVHPSDLKELADLRHF 84

Query: 64  PFTTKGDLRDSYPFGMFAVPQDRISRIHASSGTTGKPTVVGYTAADIDTWANLVARSIRA 123
           P TTK DLRD YPFGMFAVPQ+R+SRIHASSGTTG+PTVVGYT  DID WA +VARSIRA
Sbjct: 85  PHTTKADLRDHYPFGMFAVPQERVSRIHASSGTTGRPTVVGYTKDDIDAWATVVARSIRA 144

Query: 124 AGARRGDKVHVSYGYGLFTGGLGAHYGAERAGLTVIPFGGGQTEKQVQLIQDFRPDIIMV 183
           AG R G KVHV+YGYGLFTGGLGAHYGAE+ G TVIP  GGQT KQVQLIQDFRP+IIMV
Sbjct: 145 AGGRPGHKVHVAYGYGLFTGGLGAHYGAEKLGCTVIPASGGQTAKQVQLIQDFRPEIIMV 204

Query: 184 TPSYMLSIADEIERQGLDPVQSSLRIGIFGAEPWTNDMRVAIEQRMGIDAVDIYGLSEVM 243
           TPSYML++ DE ERQG+DP  +SLR+GIFGAEPWT  MR  IE+R  + AVDIYGLSEVM
Sbjct: 205 TPSYMLTLLDEFERQGVDPRTTSLRVGIFGAEPWTEQMRQEIEERFDLHAVDIYGLSEVM 264

Query: 244 GPGVASECVETKDGPTIWEDHFYPEIIDPETGEVLPDGELGELVFTSLTKEALPIIRYRT 303
           GPGVA+ECVETKDG  +WEDHF PEI+DP T EVLPDGE GEL FTSLTK+A+P+IRYRT
Sbjct: 265 GPGVANECVETKDGLHVWEDHFLPEILDPVTHEVLPDGEYGELAFTSLTKQAMPVIRYRT 324

Query: 304 RDLTRLLPGTARTMRRMEKITGRSDDMMIVRGVNVFPTQIEEQLLKQRALAPHYQIVLTK 363
           RDLT L PGTAR MRRM+K+TGRSDDM+I+RGVNVFPTQIEE +L    LAPH+Q+VLT+
Sbjct: 325 RDLTTLRPGTARPMRRMDKVTGRSDDMIILRGVNVFPTQIEEIVLGLDGLAPHFQLVLTR 384

Query: 364 EGPLDVLTLNVEPCPETAPDTAAIQVAKQALAYDIKSLIGVTAVINVLPVNGIERSVGKA 423
           EG LD + + VE  PET    A      Q +   +K  +GV+  ++V+   GIERSVGK 
Sbjct: 385 EGRLDRMAVRVEARPETT--GAQRTELAQRITATVKDRVGVSVTVDVVDPEGIERSVGKF 442

Query: 424 RRVVDKR 430
           RR++D+R
Sbjct: 443 RRIIDQR 449


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: 714
Number of extensions: 19
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: 451
Length adjustment: 32
Effective length of query: 400
Effective length of database: 419
Effective search space:   167600
Effective search space used:   167600
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_017600844.1 D471_RS0123270 (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.2229.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.1e-219  712.3   0.1   9.2e-219  712.1   0.1    1.0  1  lcl|NCBI__GCF_000341125.1:WP_017600844.1  D471_RS0123270 phenylacetate--Co


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000341125.1:WP_017600844.1  D471_RS0123270 phenylacetate--CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  712.1   0.1  9.2e-219  9.2e-219       1     422 []      32     449 ..      32     449 .. 0.99

  Alignments for each domain:
  == domain 1  score: 712.1 bits;  conditional E-value: 9.2e-219
                                 TIGR02155   1 eklsldelralqlerlkvsvkrayenvpayrkafdaagvkpddlkelsdlakfpltaksdlrdnypfdl 69 
                                               e++ +delralqlerl++s+++ay nvp+y+++fd+agv+p+dlkel+dl++fp t+k dlrd ypf++
  lcl|NCBI__GCF_000341125.1:WP_017600844.1  32 ERMGVDELRALQLERLRWSLEHAYTNVPFYKRTFDEAGVHPSDLKELADLRHFPHTTKADLRDHYPFGM 100
                                               67889**************************************************************** PP

                                 TIGR02155  70 lavprekvvrvhassGttGkptvvaytqkdldtwsevvarslraaGGrkgdllhnayGyGlftGGlGvh 138
                                               +avp+e+v r+hassGttG+ptvv+yt+ d+d w++vvars+raaGGr+g+++h+ayGyGlftGGlG+h
  lcl|NCBI__GCF_000341125.1:WP_017600844.1 101 FAVPQERVSRIHASSGTTGRPTVVGYTKDDIDAWATVVARSIRAAGGRPGHKVHVAYGYGLFTGGLGAH 169
                                               ********************************************************************* PP

                                 TIGR02155 139 yGaeklGatvvpisGGqtekqvqliqdfkpdiiavtpsyilalleelkrlgidpedislkvailGaepw 207
                                               yGaeklG+tv+p sGGqt kqvqliqdf+p+ii+vtpsy+l+ll+e++r+g+dp+ +sl+v+i+Gaepw
  lcl|NCBI__GCF_000341125.1:WP_017600844.1 170 YGAEKLGCTVIPASGGQTAKQVQLIQDFRPEIIMVTPSYMLTLLDEFERQGVDPRTTSLRVGIFGAEPW 238
                                               ********************************************************************* PP

                                 TIGR02155 208 teamrkelearlgikaldiyGlseviGpGvanecvetkdGlviwedhfypeiidpetgevlpdGeeGel 276
                                               te+mr+e+e+r++++a+diyGlsev+GpGvanecvetkdGl++wedhf pei+dp t evlpdGe Gel
  lcl|NCBI__GCF_000341125.1:WP_017600844.1 239 TEQMRQEIEERFDLHAVDIYGLSEVMGPGVANECVETKDGLHVWEDHFLPEILDPVTHEVLPDGEYGEL 307
                                               ********************************************************************* PP

                                 TIGR02155 277 vfttltkealpviryrtrdltrllpgtartmrrmdkikGrsddllilrGvnvfptqleevllkldklsp 345
                                                ft+ltk+a+pviryrtrdlt l pgtar+mrrmdk++Grsdd++ilrGvnvfptq+ee++l+ld l+p
  lcl|NCBI__GCF_000341125.1:WP_017600844.1 308 AFTSLTKQAMPVIRYRTRDLTTLRPGTARPMRRMDKVTGRSDDMIILRGVNVFPTQIEEIVLGLDGLAP 376
                                               ********************************************************************* PP

                                 TIGR02155 346 hyqleltreGaldeltlkvelkdesaalrlleqksllakkiekkikaevgvsvdvelvepgslerseGk 414
                                               h+ql ltreG+ld ++++ve+++e++ ++    ++ la++i  ++k+ vgvsv v +v+p  +ers Gk
  lcl|NCBI__GCF_000341125.1:WP_017600844.1 377 HFQLVLTREGRLDRMAVRVEARPETTGAQ----RTELAQRITATVKDRVGVSVTVDVVDPEGIERSVGK 441
                                               **********************9987665....7889******************************** PP

                                 TIGR02155 415 akrvvdkr 422
                                                +r++d+r
  lcl|NCBI__GCF_000341125.1:WP_017600844.1 442 FRRIIDQR 449
                                               ******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (422 nodes)
Target sequences:                          1  (451 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 8.69
//
[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