Alignments for a candidate for pobA in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for pobA in Pseudomonas fluorescens GW456-L13

Align 4-hydroxybenzoate 3-monooxygenase (EC 1.14.13.2) (characterized)
to candidate PfGW456L13_1787 P-hydroxybenzoate hydroxylase (EC 1.14.13.2)

Query= reanno::pseudo6_N2E2:Pf6N2E2_2914
         (396 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1787
          Length = 397

 Score =  691 bits (1784), Expect = 0.0
 Identities = 339/397 (85%), Positives = 363/397 (91%), Gaps = 1/397 (0%)

Query: 1   MKTLKTQVAIIGAGPSGLLLGQLLHNAGIDTVILERQTPEYVLSRIRAGVLEQGMVELLR 60
           MKTLKTQVAIIGAGPSGLLLGQLLHNAGID ++LERQTP+YVL RIRAGVLEQGMVELLR
Sbjct: 1   MKTLKTQVAIIGAGPSGLLLGQLLHNAGIDNIVLERQTPDYVLGRIRAGVLEQGMVELLR 60

Query: 61  QAGVGQRMDAEGLPHDGFELVLNDRRVHIDLKGLTGGKNVMVYGQTEVTRDLMAAREAAG 120
           QAGV QRMDAEGL H GFEL L+ R+VHIDL+ LTGGK VM+YGQTEVTRDLMAAR   G
Sbjct: 61  QAGVSQRMDAEGLVHGGFELALDGRQVHIDLQALTGGKTVMIYGQTEVTRDLMAARREVG 120

Query: 121 ARTLYLASNAQPHDMQTQTPFVTFEHEGETWRLDCDYIAGCDGFHGVARQSIPAEKLKVF 180
           A+T+Y ASN  PH M+T   FVTFE +GE +RLDCDYIAGCDGFHGVARQSIPA+ LKVF
Sbjct: 121 AQTIYQASNVVPHGMKTDEAFVTFEKDGEPYRLDCDYIAGCDGFHGVARQSIPADSLKVF 180

Query: 181 ERVYPFGWLGVLADTPPVHEELVYARHTRGFALCSMRSKTRTRYYLQVPAEEQVADWPDE 240
           ER+YPFGWLG+LADTPPVHEELVYARH RGFALCSMRS TRTRYYLQVPAEE V DW D+
Sbjct: 181 ERIYPFGWLGILADTPPVHEELVYARHERGFALCSMRSPTRTRYYLQVPAEENVEDWSDQ 240

Query: 241 RFWGELKNRLPADLAAALVTGPSIEKSIAPLRSFVVEPMQYGRMFLVGDAAHIVPPTGAK 300
           RFW ELKNRLP DLA  LVTGPSIEKSIAPLRSFVVEPMQYGRMFLVGDAAHIVPPTGAK
Sbjct: 241 RFWDELKNRLPVDLAQKLVTGPSIEKSIAPLRSFVVEPMQYGRMFLVGDAAHIVPPTGAK 300

Query: 301 GLNLAASDVSTLFNILLKVYRDGRVELLEKYSAICLRRVWKAERFSWWMTSMLHRFDD-D 359
           GLNLAASDVSTLFNIL+KVYRD R++LLEKYS ICLRRVWKAERFSWWMTSMLHRFDD D
Sbjct: 301 GLNLAASDVSTLFNILVKVYRDDRLDLLEKYSEICLRRVWKAERFSWWMTSMLHRFDDHD 360

Query: 360 AFNQRISEAELEYFVDSEAGRKTIAENYVGLPYEAIE 396
           AF+QRI+E+EL+YFVDS+AGRKTIAENYVGLPYEAIE
Sbjct: 361 AFSQRIAESELDYFVDSQAGRKTIAENYVGLPYEAIE 397


Lambda     K      H
   0.321    0.137    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: 622
Number of extensions: 12
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: 396
Length of database: 397
Length adjustment: 31
Effective length of query: 365
Effective length of database: 366
Effective search space:   133590
Effective search space used:   133590
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 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate PfGW456L13_1787 (P-hydroxybenzoate hydroxylase (EC 1.14.13.2))
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.11938.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   6.7e-210  682.7   0.0   7.7e-210  682.5   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1787  P-hydroxybenzoate hydroxylase (E


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1787  P-hydroxybenzoate hydroxylase (EC 1.14.13.2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  682.5   0.0  7.7e-210  7.7e-210       1     390 []       4     393 ..       4     393 .. 1.00

  Alignments for each domain:
  == domain 1  score: 682.5 bits;  conditional E-value: 7.7e-210
                                               TIGR02360   1 mktqvaiigaGpsGlllgqllhkaGidavilerksrdyvlgriraGvleqgtvdl 55 
                                                             +ktqvaiigaGpsGlllgqllh+aGid+++ler+++dyvlgriraGvleqg+v+l
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1787   4 LKTQVAIIGAGPSGLLLGQLLHNAGIDNIVLERQTPDYVLGRIRAGVLEQGMVEL 58 
                                                             69***************************************************** PP

                                               TIGR02360  56 leeagvderldreglvheGveiafegekvrvdlkkltggksvlvyGqtevtrdly 110
                                                             l++agv++r+d+eglvh G+e+a +g++v++dl++ltggk+v++yGqtevtrdl+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1787  59 LRQAGVSQRMDAEGLVHGGFELALDGRQVHIDLQALTGGKTVMIYGQTEVTRDLM 113
                                                             ******************************************************* PP

                                               TIGR02360 111 eareaaglktvyeadevrlhdlesdrpkvtfekdgeekrldcdfiaGcdGfhGvs 165
                                                              ar ++g++t+y+a +v +h +++d+  vtfekdge +rldcd+iaGcdGfhGv+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1787 114 AARREVGAQTIYQASNVVPHGMKTDEAFVTFEKDGEPYRLDCDYIAGCDGFHGVA 168
                                                             ******************************************************* PP

                                               TIGR02360 166 rksipaeklkefekvypfGwlGilsetppvsdeliysnserGfalcslrsetrsr 220
                                                             r+sipa+ lk+fe++ypfGwlGil++tppv++el+y+++erGfalcs+rs tr+r
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1787 169 RQSIPADSLKVFERIYPFGWLGILADTPPVHEELVYARHERGFALCSMRSPTRTR 223
                                                             ******************************************************* PP

                                               TIGR02360 221 yyvqvsltdkvedwsddrfweelkrrldeeaaeklvtgpsieksiaplrsfvaep 275
                                                             yy+qv+ +++vedwsd+rfw+elk+rl+ + a+klvtgpsieksiaplrsfv+ep
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1787 224 YYLQVPAEENVEDWSDQRFWDELKNRLPVDLAQKLVTGPSIEKSIAPLRSFVVEP 278
                                                             ******************************************************* PP

                                               TIGR02360 276 mryGrlflaGdaahivpptGakGlnlaasdvaylyealleaykekdsaglerysa 330
                                                             m+yGr+fl+GdaahivpptGakGlnlaasdv++l++ l++ y++ + + le+ys+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1787 279 MQYGRMFLVGDAAHIVPPTGAKGLNLAASDVSTLFNILVKVYRDDRLDLLEKYSE 333
                                                             ******************************************************* PP

                                               TIGR02360 331 kalarvwkaerfswwltsllhrfpdedefdkkiqqaeleylleseaaqktlaeny 385
                                                              +l+rvwkaerfsww+ts+lhrf+d+d+f+++i ++el+y+++s+a++kt+aeny
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1787 334 ICLRRVWKAERFSWWMTSMLHRFDDHDAFSQRIAESELDYFVDSQAGRKTIAENY 388
                                                             ******************************************************* PP

                                               TIGR02360 386 vGlpy 390
                                                             vGlpy
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1787 389 VGLPY 393
                                                             ****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (390 nodes)
Target sequences:                          1  (397 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: 9.08
//
[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