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.9869.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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 8.98
//
[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:

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:

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:

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:

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