Alignments for a candidate for pobA in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for pobA in Klebsiella michiganensis M5al

Align p-hydroxybenzoate hydroxylase (EC 1.14.13.2) (characterized)
to candidate BWI76_RS04020 BWI76_RS04020 4-hydroxybenzoate 3-monooxygenase

Query= metacyc::MONOMER-11506
         (395 letters)



>FitnessBrowser__Koxy:BWI76_RS04020
          Length = 394

 Score =  591 bits (1524), Expect = e-173
 Identities = 296/395 (74%), Positives = 333/395 (84%), Gaps = 1/395 (0%)

Query: 1   MKTQVAIIGAGPSGLLLGQLLHNAGIETVIVERQTPEYVLGRIRAGVLEQGTVDLLREAG 60
           MKTQVAIIGAGPSGLLLGQLLH+AGI+TVI+ERQTPEYVLGRIRAG+LE GTV+LLREAG
Sbjct: 1   MKTQVAIIGAGPSGLLLGQLLHHAGIQTVILERQTPEYVLGRIRAGILESGTVELLREAG 60

Query: 61  VSARMDREGLVHEGVELLVGGRRQRLDLKALTGGKTVMVYGQTEVTRDLMQAREASGAPI 120
            + RMD EGL+H GVE L  G+R  + L  LT GK+VMVYGQTEVTRDLM AR  SGAP 
Sbjct: 61  AARRMDAEGLIHHGVEFLFEGKRVPVALTELTEGKSVMVYGQTEVTRDLMAARAESGAPT 120

Query: 121 IYAANNVQPHELKGERPYLTFEKDGQAHRLECDYIAGCDGFHGVSRQSIPEGVLKQYERV 180
           IY  ++V  ++ K +RP ++F  +G+ HRLECD+IAGCDGFHGVSRQSIP GVLK+YE V
Sbjct: 121 IYGVSDVTINDAKSDRPSVSFACNGENHRLECDFIAGCDGFHGVSRQSIPAGVLKEYESV 180

Query: 181 YPFGWLGLLSDTPPVNHELIYAHHERGFALCSQRSQTRSRYYLQVPLDDKVEAWSDERFW 240
           +PFGWLGLL+DTPPVN ELIYAHHERGF LCSQRS TRSRYYLQVPL +KVEAWSDERFW
Sbjct: 181 WPFGWLGLLADTPPVNPELIYAHHERGFVLCSQRSLTRSRYYLQVPLSEKVEAWSDERFW 240

Query: 241 DELKARLPAEVAADLVTGPALEKSIAPLRSLVVEPMQYGHLFLVGDAAHIVPPTGAKGLN 300
           +ELK RLP E+++ LVTG +LEKSIAPLRS VVEPMQYG LFL+GDAAHIVPPTGAKGLN
Sbjct: 241 NELKRRLPDELSSKLVTGHSLEKSIAPLRSYVVEPMQYGKLFLLGDAAHIVPPTGAKGLN 300

Query: 301 LAASDVNYLYRILVKVYGEGRTDLLQQYSPLALRRVWKGERFSWFMTQLLHDFGSHKDAW 360
           LAASDVNYL+RIL + Y  GR DLL  YS LAL RVWKGERFSWFMT+LLHDF    + +
Sbjct: 301 LAASDVNYLWRILREYYHHGRVDLLASYSRLALDRVWKGERFSWFMTRLLHDFPQQSE-F 359

Query: 361 DQKMQEADREYFLNSPAGLLNIAENYVGLPYEAVV 395
           D+KMQ ADR Y+L S AGL  IAENYVGLP E VV
Sbjct: 360 DRKMQAADRRYYLQSRAGLTTIAENYVGLPMERVV 394


Lambda     K      H
   0.320    0.138    0.415 

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: 606
Number of extensions: 25
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: 395
Length of database: 394
Length adjustment: 31
Effective length of query: 364
Effective length of database: 363
Effective search space:   132132
Effective search space used:   132132
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: 50 (23.9 bits)

Align candidate BWI76_RS04020 BWI76_RS04020 (4-hydroxybenzoate 3-monooxygenase)
to HMM TIGR02360 (pobA: 4-hydroxybenzoate 3-monooxygenase (EC 1.14.13.2))

# 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/TIGR02360.hmm
# target sequence database:        /tmp/gapView.1559.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02360  [M=390]
Accession:   TIGR02360
Description: pbenz_hydroxyl: 4-hydroxybenzoate 3-monooxygenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
     2e-197  641.7   0.0   2.2e-197  641.5   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS04020  BWI76_RS04020 4-hydroxybenzoate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS04020  BWI76_RS04020 4-hydroxybenzoate 3-monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  641.5   0.0  2.2e-197  2.2e-197       1     390 []       1     390 [.       1     390 [. 1.00

  Alignments for each domain:
  == domain 1  score: 641.5 bits;  conditional E-value: 2.2e-197
                               TIGR02360   1 mktqvaiigaGpsGlllgqllhkaGidavilerksrdyvlgriraGvleqgtvdlleeagvderldreglv 71 
                                             mktqvaiigaGpsGlllgqllh+aGi++viler++++yvlgriraG+le+gtv+ll+eag+++r+d+egl+
  lcl|FitnessBrowser__Koxy:BWI76_RS04020   1 MKTQVAIIGAGPSGLLLGQLLHHAGIQTVILERQTPEYVLGRIRAGILESGTVELLREAGAARRMDAEGLI 71 
                                             9********************************************************************** PP

                               TIGR02360  72 heGveiafegekvrvdlkkltggksvlvyGqtevtrdlyeareaaglktvyeadevrlhdlesdrpkvtfe 142
                                             h+Gve  feg++v v l++lt+gksv+vyGqtevtrdl+ ar + g+ t+y + +v+++d++sdrp v+f 
  lcl|FitnessBrowser__Koxy:BWI76_RS04020  72 HHGVEFLFEGKRVPVALTELTEGKSVMVYGQTEVTRDLMAARAESGAPTIYGVSDVTINDAKSDRPSVSFA 142
                                             *********************************************************************** PP

                               TIGR02360 143 kdgeekrldcdfiaGcdGfhGvsrksipaeklkefekvypfGwlGilsetppvsdeliysnserGfalcsl 213
                                              +ge++rl+cdfiaGcdGfhGvsr+sipa +lke+e v+pfGwlG+l++tppv+ eliy+++erGf lcs+
  lcl|FitnessBrowser__Koxy:BWI76_RS04020 143 CNGENHRLECDFIAGCDGFHGVSRQSIPAGVLKEYESVWPFGWLGLLADTPPVNPELIYAHHERGFVLCSQ 213
                                             *********************************************************************** PP

                               TIGR02360 214 rsetrsryyvqvsltdkvedwsddrfweelkrrldeeaaeklvtgpsieksiaplrsfvaepmryGrlfla 284
                                             rs trsryy+qv+l++kve wsd+rfw+elkrrl++e + klvtg s+eksiaplrs+v+epm+yG+lfl 
  lcl|FitnessBrowser__Koxy:BWI76_RS04020 214 RSLTRSRYYLQVPLSEKVEAWSDERFWNELKRRLPDELSSKLVTGHSLEKSIAPLRSYVVEPMQYGKLFLL 284
                                             *********************************************************************** PP

                               TIGR02360 285 GdaahivpptGakGlnlaasdvaylyealleaykekdsaglerysakalarvwkaerfswwltsllhrfpd 355
                                             GdaahivpptGakGlnlaasdv+yl++ l+e+y++++ + l +ys  al rvwk erfsw++t+llh fp+
  lcl|FitnessBrowser__Koxy:BWI76_RS04020 285 GDAAHIVPPTGAKGLNLAASDVNYLWRILREYYHHGRVDLLASYSRLALDRVWKGERFSWFMTRLLHDFPQ 355
                                             *********************************************************************** PP

                               TIGR02360 356 edefdkkiqqaeleylleseaaqktlaenyvGlpy 390
                                             ++efd+k+q a+  y+l+s+a+++t+aenyvGlp+
  lcl|FitnessBrowser__Koxy:BWI76_RS04020 356 QSEFDRKMQAADRRYYLQSRAGLTTIAENYVGLPM 390
                                             *********************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (390 nodes)
Target sequences:                          1  (394 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: 00:00:00.01
# Mc/sec: 8.45
//
[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