Alignments for a candidate for paaK in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaK in Paraburkholderia bryophila 376MFSha3.1

Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate H281DRAFT_05720 H281DRAFT_05720 phenylacetate-CoA ligase

Query= BRENDA::B4E7B5
         (432 letters)



>FitnessBrowser__Burk376:H281DRAFT_05720
          Length = 434

 Score =  799 bits (2064), Expect = 0.0
 Identities = 397/431 (92%), Positives = 413/431 (95%)

Query: 1   MTTPLPLEPIETASRDELTALQLERLKWSLRHAYDHSPVYRRKFDEAGVHPDDLKTLADL 60
           MTT LPL+PIETASRDEL ALQLERLKWSL HAY++SPVYRRKFDEAGVHP +L TLADL
Sbjct: 1   MTTALPLDPIETASRDELCALQLERLKWSLNHAYENSPVYRRKFDEAGVHPSELTTLADL 60

Query: 61  SRFPFTTKGDLRDSYPFGMFAVPQDRISRIHASSGTTGKPTVVGYTAADIDTWANLVARS 120
           +RFPFTTK DLRDSYPFGMFAVPQDRISRIHASSGTTGKPTVVGYTA DIDTWANLVARS
Sbjct: 61  ARFPFTTKKDLRDSYPFGMFAVPQDRISRIHASSGTTGKPTVVGYTARDIDTWANLVARS 120

Query: 121 IRAAGARRGDKVHVSYGYGLFTGGLGAHYGAERAGLTVIPFGGGQTEKQVQLIQDFRPDI 180
           IRAAGA+ GDKVHVSYGYGLFTGGLGAHYGAERAGLTVIPFGGGQTEKQVQLIQDFRPDI
Sbjct: 121 IRAAGAKPGDKVHVSYGYGLFTGGLGAHYGAERAGLTVIPFGGGQTEKQVQLIQDFRPDI 180

Query: 181 IMVTPSYMLSIADEIERQGLDPVQSSLRIGIFGAEPWTNDMRVAIEQRMGIDAVDIYGLS 240
           IMVTPSYMLSIADE+ERQG+DP   SLRIGIFGAEPWTNDMR AIE+RMGIDAVDIYGLS
Sbjct: 181 IMVTPSYMLSIADELERQGVDPASCSLRIGIFGAEPWTNDMRHAIEKRMGIDAVDIYGLS 240

Query: 241 EVMGPGVASECVETKDGPTIWEDHFYPEIIDPETGEVLPDGELGELVFTSLTKEALPIIR 300
           EVMGPGVASECVETKDGPTIWEDHFYPEIIDPETGEVLPDGELGELVFTSLTKEALPIIR
Sbjct: 241 EVMGPGVASECVETKDGPTIWEDHFYPEIIDPETGEVLPDGELGELVFTSLTKEALPIIR 300

Query: 301 YRTRDLTRLLPGTARTMRRMEKITGRSDDMMIVRGVNVFPTQIEEQLLKQRALAPHYQIV 360
           YRTRDLTRLLPG+ARTMRRMEKITGRSDDMMIVRGVNVFPTQIEE LLKQ ALAPHYQIV
Sbjct: 301 YRTRDLTRLLPGSARTMRRMEKITGRSDDMMIVRGVNVFPTQIEELLLKQHALAPHYQIV 360

Query: 361 LTKEGPLDVLTLNVEPCPETAPDTAAIQVAKQALAYDIKSLIGVTAVINVLPVNGIERSV 420
           LT+EGPLDVLTLNVEPCPETAPDT+ +  AKQALAYDIK+LIGV+AV+NVL VNGIERSV
Sbjct: 361 LTREGPLDVLTLNVEPCPETAPDTSVLNTAKQALAYDIKALIGVSAVVNVLAVNGIERSV 420

Query: 421 GKARRVVDKRK 431
           GKARRVVDKRK
Sbjct: 421 GKARRVVDKRK 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: 789
Number of extensions: 10
Number of successful extensions: 1
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: 434
Length adjustment: 32
Effective length of query: 400
Effective length of database: 402
Effective search space:   160800
Effective search space used:   160800
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 H281DRAFT_05720 H281DRAFT_05720 (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.22882.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   5.8e-219  712.7   0.0   6.6e-219  712.5   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_05720  H281DRAFT_05720 phenylacetate-Co


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_05720  H281DRAFT_05720 phenylacetate-CoA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  712.5   0.0  6.6e-219  6.6e-219       1     422 []      11     430 ..      11     430 .. 0.99

  Alignments for each domain:
  == domain 1  score: 712.5 bits;  conditional E-value: 6.6e-219
                                    TIGR02155   1 eklsldelralqlerlkvsvkrayenvpayrkafdaagvkpddlkelsdlakfpltaksdlrdnyp 66 
                                                  e++s+del alqlerlk+s+++ayen p+yr++fd+agv+p++l +l+dla+fp+t+k+dlrd yp
  lcl|FitnessBrowser__Burk376:H281DRAFT_05720  11 ETASRDELCALQLERLKWSLNHAYENSPVYRRKFDEAGVHPSELTTLADLARFPFTTKKDLRDSYP 76 
                                                  89**************************************************************** PP

                                    TIGR02155  67 fdllavprekvvrvhassGttGkptvvaytqkdldtwsevvarslraaGGrkgdllhnayGyGlft 132
                                                  f+++avp++++ r+hassGttGkptvv+yt++d+dtw+++vars+raaG ++gd++h++yGyGlft
  lcl|FitnessBrowser__Burk376:H281DRAFT_05720  77 FGMFAVPQDRISRIHASSGTTGKPTVVGYTARDIDTWANLVARSIRAAGAKPGDKVHVSYGYGLFT 142
                                                  ****************************************************************** PP

                                    TIGR02155 133 GGlGvhyGaeklGatvvpisGGqtekqvqliqdfkpdiiavtpsyilalleelkrlgidpedislk 198
                                                  GGlG+hyGae+ G tv+p+ GGqtekqvqliqdf+pdii+vtpsy+l++++el+r+g+dp+++sl+
  lcl|FitnessBrowser__Burk376:H281DRAFT_05720 143 GGLGAHYGAERAGLTVIPFGGGQTEKQVQLIQDFRPDIIMVTPSYMLSIADELERQGVDPASCSLR 208
                                                  ****************************************************************** PP

                                    TIGR02155 199 vailGaepwteamrkelearlgikaldiyGlseviGpGvanecvetkdGlviwedhfypeiidpet 264
                                                  ++i+Gaepwt++mr+++e+r+gi+a+diyGlsev+GpGva ecvetkdG++iwedhfypeiidpet
  lcl|FitnessBrowser__Burk376:H281DRAFT_05720 209 IGIFGAEPWTNDMRHAIEKRMGIDAVDIYGLSEVMGPGVASECVETKDGPTIWEDHFYPEIIDPET 274
                                                  ****************************************************************** PP

                                    TIGR02155 265 gevlpdGeeGelvfttltkealpviryrtrdltrllpgtartmrrmdkikGrsddllilrGvnvfp 330
                                                  gevlpdGe Gelvft+ltkealp+iryrtrdltrllpg+artmrrm+ki+Grsdd++i+rGvnvfp
  lcl|FitnessBrowser__Burk376:H281DRAFT_05720 275 GEVLPDGELGELVFTSLTKEALPIIRYRTRDLTRLLPGSARTMRRMEKITGRSDDMMIVRGVNVFP 340
                                                  ****************************************************************** PP

                                    TIGR02155 331 tqleevllkldklsphyqleltreGaldeltlkvelkdesaalrlleqksllakkiekkikaevgv 396
                                                  tq+ee+llk++ l+phyq+ ltreG ld ltl+ve  +e+a  ++  +  + ++ +  +ika +gv
  lcl|FitnessBrowser__Burk376:H281DRAFT_05720 341 TQIEELLLKQHALAPHYQIVLTREGPLDVLTLNVEPCPETAPDTSVLN--TAKQALAYDIKALIGV 404
                                                  **************************************9987775544..46899*********** PP

                                    TIGR02155 397 svdvelvepgslerseGkakrvvdkr 422
                                                  s+ v++ +   +ers Gka+rvvdkr
  lcl|FitnessBrowser__Burk376:H281DRAFT_05720 405 SAVVNVLAVNGIERSVGKARRVVDKR 430
                                                  *************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (422 nodes)
Target sequences:                          1  (434 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.77
//
[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