Alignments for a candidate for tnaA in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for tnaA in Escherichia coli BW25113

Align tryptophanase (EC 4.1.99.1) (characterized)
to candidate 17768 b3708 tryptophanase (VIMSS)

Query= BRENDA::P0A853
         (471 letters)



>FitnessBrowser__Keio:17768
          Length = 471

 Score =  948 bits (2450), Expect = 0.0
 Identities = 471/471 (100%), Positives = 471/471 (100%)

Query: 1   MENFKHLPEPFRIRVIEPVKRTTRAYREEAIIKSGMNPFLLDSEDVFIDLLTDSGTGAVT 60
           MENFKHLPEPFRIRVIEPVKRTTRAYREEAIIKSGMNPFLLDSEDVFIDLLTDSGTGAVT
Sbjct: 1   MENFKHLPEPFRIRVIEPVKRTTRAYREEAIIKSGMNPFLLDSEDVFIDLLTDSGTGAVT 60

Query: 61  QSMQAAMMRGDEAYSGSRSYYALAESVKNIFGYQYTIPTHQGRGAEQIYIPVLIKKREQE 120
           QSMQAAMMRGDEAYSGSRSYYALAESVKNIFGYQYTIPTHQGRGAEQIYIPVLIKKREQE
Sbjct: 61  QSMQAAMMRGDEAYSGSRSYYALAESVKNIFGYQYTIPTHQGRGAEQIYIPVLIKKREQE 120

Query: 121 KGLDRSKMVAFSNYFFDTTQGHSQINGCTVRNVYIKEAFDTGVRYDFKGNFDLEGLERGI 180
           KGLDRSKMVAFSNYFFDTTQGHSQINGCTVRNVYIKEAFDTGVRYDFKGNFDLEGLERGI
Sbjct: 121 KGLDRSKMVAFSNYFFDTTQGHSQINGCTVRNVYIKEAFDTGVRYDFKGNFDLEGLERGI 180

Query: 181 EEVGPNNVPYIVATITSNSAGGQPVSLANLKAMYSIAKKYDIPVVMDSARFAENAYFIKQ 240
           EEVGPNNVPYIVATITSNSAGGQPVSLANLKAMYSIAKKYDIPVVMDSARFAENAYFIKQ
Sbjct: 181 EEVGPNNVPYIVATITSNSAGGQPVSLANLKAMYSIAKKYDIPVVMDSARFAENAYFIKQ 240

Query: 241 REAEYKDWTIEQITRETYKYADMLAMSAKKDAMVPMGGLLCMKDDSFFDVYTECRTLCVV 300
           REAEYKDWTIEQITRETYKYADMLAMSAKKDAMVPMGGLLCMKDDSFFDVYTECRTLCVV
Sbjct: 241 REAEYKDWTIEQITRETYKYADMLAMSAKKDAMVPMGGLLCMKDDSFFDVYTECRTLCVV 300

Query: 301 QEGFPTYGGLEGGAMERLAVGLYDGMNLDWLAYRIAQVQYLVDGLEEIGVVCQQAGGHAA 360
           QEGFPTYGGLEGGAMERLAVGLYDGMNLDWLAYRIAQVQYLVDGLEEIGVVCQQAGGHAA
Sbjct: 301 QEGFPTYGGLEGGAMERLAVGLYDGMNLDWLAYRIAQVQYLVDGLEEIGVVCQQAGGHAA 360

Query: 361 FVDAGKLLPHIPADQFPAQALACELYKVAGIRAVEIGSFLLGRDPKTGKQLPCPAELLRL 420
           FVDAGKLLPHIPADQFPAQALACELYKVAGIRAVEIGSFLLGRDPKTGKQLPCPAELLRL
Sbjct: 361 FVDAGKLLPHIPADQFPAQALACELYKVAGIRAVEIGSFLLGRDPKTGKQLPCPAELLRL 420

Query: 421 TIPRATYTQTHMDFIIEAFKHVKENAANIKGLTFTYEPKVLRHFTAKLKEV 471
           TIPRATYTQTHMDFIIEAFKHVKENAANIKGLTFTYEPKVLRHFTAKLKEV
Sbjct: 421 TIPRATYTQTHMDFIIEAFKHVKENAANIKGLTFTYEPKVLRHFTAKLKEV 471


Lambda     K      H
   0.320    0.137    0.402 

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: 913
Number of extensions: 15
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: 471
Length of database: 471
Length adjustment: 33
Effective length of query: 438
Effective length of database: 438
Effective search space:   191844
Effective search space used:   191844
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 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate 17768 b3708 (tryptophanase (VIMSS))
to HMM TIGR02617 (tnaA: tryptophanase (EC 4.1.99.1))

# 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/TIGR02617.hmm
# target sequence database:        /tmp/gapView.9882.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02617  [M=467]
Accession:   TIGR02617
Description: tnaA_trp_ase: tryptophanase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
          0 1010.2   0.3          0 1010.0   0.3    1.0  1  lcl|FitnessBrowser__Keio:17768  b3708 tryptophanase (VIMSS)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:17768  b3708 tryptophanase (VIMSS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1010.0   0.3         0         0       1     467 []       5     471 .]       5     471 .] 1.00

  Alignments for each domain:
  == domain 1  score: 1010.0 bits;  conditional E-value: 0
                       TIGR02617   1 krlpepfrirviepvkrttraerekalleaglnpflldsedvfidlltdsgtgavtdemqaallrgdeaysgsrsyyal 79 
                                     k+lpepfrirviepvkrttra+re+a++++g+npflldsedvfidlltdsgtgavt++mqaa++rgdeaysgsrsyyal
  lcl|FitnessBrowser__Keio:17768   5 KHLPEPFRIRVIEPVKRTTRAYREEAIIKSGMNPFLLDSEDVFIDLLTDSGTGAVTQSMQAAMMRGDEAYSGSRSYYAL 83 
                                     8****************************************************************************** PP

                       TIGR02617  80 aekvkellgyqytipthqgrgaeqiyipvlikkrekekgldrskmvalsnyffdttqghvelngakaknvyteeafdtg 158
                                     ae+vk+++gyqytipthqgrgaeqiyipvlikkre+ekgldrskmva+snyffdttqgh+++ng++++nvy++eafdtg
  lcl|FitnessBrowser__Keio:17768  84 AESVKNIFGYQYTIPTHQGRGAEQIYIPVLIKKREQEKGLDRSKMVAFSNYFFDTTQGHSQINGCTVRNVYIKEAFDTG 162
                                     ******************************************************************************* PP

                       TIGR02617 159 vkydfkgdfdleelekaiaeagadnvvyivatitcnsaggqpvslanlkavyeiakkydipvvldsarfaenayfikqr 237
                                     v+ydfkg+fdle+le++i+e+g++nv+yivatit+nsaggqpvslanlka+y+iakkydipvv+dsarfaenayfikqr
  lcl|FitnessBrowser__Keio:17768 163 VRYDFKGNFDLEGLERGIEEVGPNNVPYIVATITSNSAGGQPVSLANLKAMYSIAKKYDIPVVMDSARFAENAYFIKQR 241
                                     ******************************************************************************* PP

                       TIGR02617 238 ekeyknksieqivreaykyadmlamsakkdalvnlggllclkddsffdvytevrtlcvvqegfvtyggleggamerlav 316
                                     e+eyk+++ieqi+re+ykyadmlamsakkda+v++ggllc+kddsffdvyte+rtlcvvqegf+tyggleggamerlav
  lcl|FitnessBrowser__Keio:17768 242 EAEYKDWTIEQITRETYKYADMLAMSAKKDAMVPMGGLLCMKDDSFFDVYTECRTLCVVQEGFPTYGGLEGGAMERLAV 320
                                     ******************************************************************************* PP

                       TIGR02617 317 gledgmnedylayrinqveylvngleeigvviqqagghaafvdakkllphipadqfpahalacelykvagiraveigsl 395
                                     gl+dgmn d+layri+qv+ylv+gleeigvv+qqagghaafvda+kllphipadqfpa+alacelykvagiraveigs+
  lcl|FitnessBrowser__Keio:17768 321 GLYDGMNLDWLAYRIAQVQYLVDGLEEIGVVCQQAGGHAAFVDAGKLLPHIPADQFPAQALACELYKVAGIRAVEIGSF 399
                                     ******************************************************************************* PP

                       TIGR02617 396 llgrdpktgkqkpspaellrltipravytqthmdfiieafkkvkenaanikgltftyepkvlrhfvarlkev 467
                                     llgrdpktgkq p+paellrltipra+ytqthmdfiieafk+vkenaanikgltftyepkvlrhf+a+lkev
  lcl|FitnessBrowser__Keio:17768 400 LLGRDPKTGKQLPCPAELLRLTIPRATYTQTHMDFIIEAFKHVKENAANIKGLTFTYEPKVLRHFTAKLKEV 471
                                     **********************************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (467 nodes)
Target sequences:                          1  (471 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: 00:00:00.03
# Mc/sec: 6.94
//
[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