Alignments for a candidate for tnaA in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for tnaA in Klebsiella michiganensis M5al

Align Tryptophanase (EC 4.1.99.1) (characterized)
to candidate BWI76_RS03535 BWI76_RS03535 tryptophanase

Query= reanno::Koxy:BWI76_RS03535
         (462 letters)



>FitnessBrowser__Koxy:BWI76_RS03535
          Length = 462

 Score =  936 bits (2419), Expect = 0.0
 Identities = 462/462 (100%), Positives = 462/462 (100%)

Query: 1   MKRIPEPFRIKMVENIRMTTFDDRVKALEEAGYNPFLLNSQDVYIDLLTDSGTGAMSDHQ 60
           MKRIPEPFRIKMVENIRMTTFDDRVKALEEAGYNPFLLNSQDVYIDLLTDSGTGAMSDHQ
Sbjct: 1   MKRIPEPFRIKMVENIRMTTFDDRVKALEEAGYNPFLLNSQDVYIDLLTDSGTGAMSDHQ 60

Query: 61  WAGLMMGDEAYAGSRNYQHLCEKVKEIIGYPYTIPTHQGRGAEQILFPSLIARRKSAHPV 120
           WAGLMMGDEAYAGSRNYQHLCEKVKEIIGYPYTIPTHQGRGAEQILFPSLIARRKSAHPV
Sbjct: 61  WAGLMMGDEAYAGSRNYQHLCEKVKEIIGYPYTIPTHQGRGAEQILFPSLIARRKSAHPV 120

Query: 121 FISNFHFDTTAAHVELNGAKAINVVTPKAFDTTSWYDWKGNFDIVLLKATIAEHGAENVA 180
           FISNFHFDTTAAHVELNGAKAINVVTPKAFDTTSWYDWKGNFDIVLLKATIAEHGAENVA
Sbjct: 121 FISNFHFDTTAAHVELNGAKAINVVTPKAFDTTSWYDWKGNFDIVLLKATIAEHGAENVA 180

Query: 181 AIITTVTCNSSGGQPVSLANMREVYQIARQNNIPVVIDSARFCENAWFIKQREEGYADKS 240
           AIITTVTCNSSGGQPVSLANMREVYQIARQNNIPVVIDSARFCENAWFIKQREEGYADKS
Sbjct: 181 AIITTVTCNSSGGQPVSLANMREVYQIARQNNIPVVIDSARFCENAWFIKQREEGYADKS 240

Query: 241 VKEIILEMYQYGDMLTMSAKKDPMVNIGGLCCFRDDEDLFNEVRIRCVPMEGFVTYGGLA 300
           VKEIILEMYQYGDMLTMSAKKDPMVNIGGLCCFRDDEDLFNEVRIRCVPMEGFVTYGGLA
Sbjct: 241 VKEIILEMYQYGDMLTMSAKKDPMVNIGGLCCFRDDEDLFNEVRIRCVPMEGFVTYGGLA 300

Query: 301 GRDMEALAIGLEEGTNEDYLAYRINQVEYLGERLREGGIPIQYPTGGHAVFVDAKLLLPH 360
           GRDMEALAIGLEEGTNEDYLAYRINQVEYLGERLREGGIPIQYPTGGHAVFVDAKLLLPH
Sbjct: 301 GRDMEALAIGLEEGTNEDYLAYRINQVEYLGERLREGGIPIQYPTGGHAVFVDAKLLLPH 360

Query: 361 IPPEQFPAHALNNELYLEAGIRSVEIGSLLLGRDPQTGKQKASPMELLRLTIPRRVYTND 420
           IPPEQFPAHALNNELYLEAGIRSVEIGSLLLGRDPQTGKQKASPMELLRLTIPRRVYTND
Sbjct: 361 IPPEQFPAHALNNELYLEAGIRSVEIGSLLLGRDPQTGKQKASPMELLRLTIPRRVYTND 420

Query: 421 HMDYIADALIAVKARAATIKGLTFTYEPPVLRHFVARLKPVK 462
           HMDYIADALIAVKARAATIKGLTFTYEPPVLRHFVARLKPVK
Sbjct: 421 HMDYIADALIAVKARAATIKGLTFTYEPPVLRHFVARLKPVK 462


Lambda     K      H
   0.321    0.138    0.411 

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: 862
Number of extensions: 19
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: 462
Length of database: 462
Length adjustment: 33
Effective length of query: 429
Effective length of database: 429
Effective search space:   184041
Effective search space used:   184041
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 BWI76_RS03535 BWI76_RS03535 (tryptophanase)
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.30189.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   2.3e-260  850.3   0.0   2.6e-260  850.1   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS03535  BWI76_RS03535 tryptophanase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS03535  BWI76_RS03535 tryptophanase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  850.1   0.0  2.6e-260  2.6e-260       1     467 []       2     461 ..       2     461 .. 0.99

  Alignments for each domain:
  == domain 1  score: 850.1 bits;  conditional E-value: 2.6e-260
                               TIGR02617   1 krlpepfrirviepvkrttraerekalleaglnpflldsedvfidlltdsgtgavtdemqaallrgdeays 71 
                                             kr+pepfri+++e++++tt ++r kal+eag+npfll+s+dv+idlltdsgtga++d+++a+l++gdeay+
  lcl|FitnessBrowser__Koxy:BWI76_RS03535   2 KRIPEPFRIKMVENIRMTTFDDRVKALEEAGYNPFLLNSQDVYIDLLTDSGTGAMSDHQWAGLMMGDEAYA 72 
                                             89********************************************************************* PP

                               TIGR02617  72 gsrsyyalaekvkellgyqytipthqgrgaeqiyipvlikkrekekgldrskmvalsnyffdttqghveln 142
                                             gsr+y +l+ekvke++gy ytipthqgrgaeqi++p li++r+      ++  v++sn++fdtt++hveln
  lcl|FitnessBrowser__Koxy:BWI76_RS03535  73 GSRNYQHLCEKVKEIIGYPYTIPTHQGRGAEQILFPSLIARRKS----AHP--VFISNFHFDTTAAHVELN 137
                                             *****************************************986....477..****************** PP

                               TIGR02617 143 gakaknvyteeafdtgvkydfkgdfdleelekaiaeagadnvvyivatitcnsaggqpvslanlkavyeia 213
                                             gaka+nv+t +afdt+  yd+kg+fd+  l+ +iae+ga+nv++i++t+tcns+ggqpvslan++ vy+ia
  lcl|FitnessBrowser__Koxy:BWI76_RS03535 138 GAKAINVVTPKAFDTTSWYDWKGNFDIVLLKATIAEHGAENVAAIITTVTCNSSGGQPVSLANMREVYQIA 208
                                             *********************************************************************** PP

                               TIGR02617 214 kkydipvvldsarfaenayfikqrekeyknksieqivreaykyadmlamsakkdalvnlggllclkddsff 284
                                             ++ +ipvv+dsarf+ena+fikqre++y +ks+++i+ e+y+y+dml+msakkd++vn+ggl+c++dd  +
  lcl|FitnessBrowser__Koxy:BWI76_RS03535 209 RQNNIPVVIDSARFCENAWFIKQREEGYADKSVKEIILEMYQYGDMLTMSAKKDPMVNIGGLCCFRDD--E 277
                                             ********************************************************************..* PP

                               TIGR02617 285 dvytevrtlcvvqegfvtyggleggamerlavgledgmnedylayrinqveylvngleeigvviqq.aggh 354
                                             d+++evr +cv++egfvtyggl+g++me+la+gle+g nedylayrinqveyl+++l+e g++iq+ +ggh
  lcl|FitnessBrowser__Koxy:BWI76_RS03535 278 DLFNEVRIRCVPMEGFVTYGGLAGRDMEALAIGLEEGTNEDYLAYRINQVEYLGERLREGGIPIQYpTGGH 348
                                             *********************************************************************** PP

                               TIGR02617 355 aafvdakkllphipadqfpahalacelykvagiraveigslllgrdpktgkqkpspaellrltipravytq 425
                                             a+fvdak+llphip +qfpahal++ely++agir+veigslllgrdp+tgkqk sp+ellrltipr+vyt+
  lcl|FitnessBrowser__Koxy:BWI76_RS03535 349 AVFVDAKLLLPHIPPEQFPAHALNNELYLEAGIRSVEIGSLLLGRDPQTGKQKASPMELLRLTIPRRVYTN 419
                                             *********************************************************************** PP

                               TIGR02617 426 thmdfiieafkkvkenaanikgltftyepkvlrhfvarlkev 467
                                             +hmd+i +a++ vk++aa ikgltftyep+vlrhfvarlk+v
  lcl|FitnessBrowser__Koxy:BWI76_RS03535 420 DHMDYIADALIAVKARAATIKGLTFTYEPPVLRHFVARLKPV 461
                                             ****************************************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (467 nodes)
Target sequences:                          1  (462 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: 11.04
//
[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