Alignments for a candidate for kyn in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for kyn in Pseudomonas fluorescens FW300-N2E3

Align Kynureninase (EC 3.7.1.3) (characterized)
to candidate AO353_05935 AO353_05935 kynureninase

Query= reanno::pseudo3_N2E3:AO353_05935
         (416 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_05935
          Length = 416

 Score =  836 bits (2160), Expect = 0.0
 Identities = 416/416 (100%), Positives = 416/416 (100%)

Query: 1   MITRNDCLALDAQDPLAHLRHQFALPEGVIYLDGNSLGARPVAALERAQAVIAEEWGNGL 60
           MITRNDCLALDAQDPLAHLRHQFALPEGVIYLDGNSLGARPVAALERAQAVIAEEWGNGL
Sbjct: 1   MITRNDCLALDAQDPLAHLRHQFALPEGVIYLDGNSLGARPVAALERAQAVIAEEWGNGL 60

Query: 61  IRSWNSAGWRDLPERLGNRLAGLIGAGEGEVVVTDTTSINLFKVLGAALRVQAMRAPTRR 120
           IRSWNSAGWRDLPERLGNRLAGLIGAGEGEVVVTDTTSINLFKVLGAALRVQAMRAPTRR
Sbjct: 61  IRSWNSAGWRDLPERLGNRLAGLIGAGEGEVVVTDTTSINLFKVLGAALRVQAMRAPTRR 120

Query: 121 VIVSESSNFPTDLYIAEGLMDLLQQGYSLRLVDSPEELAQAIDQDTAVVMLTHVNYKTGY 180
           VIVSESSNFPTDLYIAEGLMDLLQQGYSLRLVDSPEELAQAIDQDTAVVMLTHVNYKTGY
Sbjct: 121 VIVSESSNFPTDLYIAEGLMDLLQQGYSLRLVDSPEELAQAIDQDTAVVMLTHVNYKTGY 180

Query: 181 MHDMQAVTALIHECGALAIWDLAHSAGAVPVDLRQAGADYAIGCTYKYLNGGPGSQAFVW 240
           MHDMQAVTALIHECGALAIWDLAHSAGAVPVDLRQAGADYAIGCTYKYLNGGPGSQAFVW
Sbjct: 181 MHDMQAVTALIHECGALAIWDLAHSAGAVPVDLRQAGADYAIGCTYKYLNGGPGSQAFVW 240

Query: 241 VAPQLCDLVTQPLSGWFGHSRQFDMASGYEPSSGIARYLCGTQPITSLAMVECGLEIFAQ 300
           VAPQLCDLVTQPLSGWFGHSRQFDMASGYEPSSGIARYLCGTQPITSLAMVECGLEIFAQ
Sbjct: 241 VAPQLCDLVTQPLSGWFGHSRQFDMASGYEPSSGIARYLCGTQPITSLAMVECGLEIFAQ 300

Query: 301 TDMPSLRRKSLALTDLFIQLVEQRCAAHDLKLITPREHARRGSHVSFEHPQGYAVIQALI 360
           TDMPSLRRKSLALTDLFIQLVEQRCAAHDLKLITPREHARRGSHVSFEHPQGYAVIQALI
Sbjct: 301 TDMPSLRRKSLALTDLFIQLVEQRCAAHDLKLITPREHARRGSHVSFEHPQGYAVIQALI 360

Query: 361 AQGVIGDYREPRIMRFGFTPLYTSFTEVFDAVQILGEILDQQTWSQAQFQVRHSVT 416
           AQGVIGDYREPRIMRFGFTPLYTSFTEVFDAVQILGEILDQQTWSQAQFQVRHSVT
Sbjct: 361 AQGVIGDYREPRIMRFGFTPLYTSFTEVFDAVQILGEILDQQTWSQAQFQVRHSVT 416


Lambda     K      H
   0.322    0.136    0.413 

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: 788
Number of extensions: 27
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: 416
Length of database: 416
Length adjustment: 31
Effective length of query: 385
Effective length of database: 385
Effective search space:   148225
Effective search space used:   148225
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 AO353_05935 AO353_05935 (kynureninase)
to HMM TIGR01814 (kynU: kynureninase (EC 3.7.1.3))

# 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/TIGR01814.hmm
# target sequence database:        /tmp/gapView.1011921.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01814  [M=400]
Accession:   TIGR01814
Description: kynureninase: kynureninase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.1e-108  348.7   0.0   2.6e-108  348.4   0.0    1.1  1  FitnessBrowser__pseudo3_N2E3:AO353_05935  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__pseudo3_N2E3:AO353_05935  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  348.4   0.0  2.6e-108  2.6e-108       2     400 .]       8     400 ..       7     400 .. 0.91

  Alignments for each domain:
  == domain 1  score: 348.4 bits;  conditional E-value: 2.6e-108
                                 TIGR01814   2 ealdaadelkalRdeFalpkakdeneviyld.NSLalmp.kaakealkeeldkWakllveshevgkapW 68 
                                                alda+d+l++lR +Falp     + viyld NSL++ p +a+++a+  ++++W++ l++s++  +a W
  FitnessBrowser__pseudo3_N2E3:AO353_05935   8 LALDAQDPLAHLRHQFALP-----EGVIYLDgNSLGARPvAALERAQAVIAEEWGNGLIRSWN--SAGW 69 
                                               78*****************.....99****66***9988356788999999************..999* PP

                                 TIGR01814  69 leldealeklla..lvakekevvvmnsltvNlhkllasfykp....tekRakIlleakaFPsDlyaies 131
                                                +l+e+l + la  ++a e evvv++++++Nl+k+l +++++    +++R++I++e+++FP+Dly++e 
  FitnessBrowser__pseudo3_N2E3:AO353_05935  70 RDLPERLGNRLAglIGAGEGEVVVTDTTSINLFKVLGAALRVqamrAPTRRVIVSESSNFPTDLYIAEG 138
                                               *******999888999************************9888889*********************9 PP

                                 TIGR01814 132 qlklkleveeslvqvepreeetlrledildviekeqdeiAlvllsgvqYkt.qlfdlaaitkaarkkga 199
                                                + l  ++  sl+ v++ e          ++ ++ +++ A+v+l++v+Ykt  + d++a+t++ ++ ga
  FitnessBrowser__pseudo3_N2E3:AO353_05935 139 LMDLL-QQGYSLRLVDSPE----------ELAQAIDQDTAVVMLTHVNYKTgYMHDMQAVTALIHECGA 196
                                               99998.5555565555555..........3334456679************999*************** PP

                                 TIGR01814 200 lvvfDLaHava.vpleLhdwdvDfAvwCsYKylnaspaagafvhekkakeelprlalwwwhekskrfkm 267
                                               l+++DLaH+++ vp++L ++++D+A+ C+YKyln +p + afv+ ++   +l+ ++l+ w  +s +f+m
  FitnessBrowser__pseudo3_N2E3:AO353_05935 197 LAIWDLAHSAGaVPVDLRQAGADYAIGCTYKYLNGGPGSQAFVWVAPQLCDLVTQPLSGWFGHSRQFDM 265
                                               **********99*************************999*******9999998876555555566666 PP

                                 TIGR01814 268 eeklelrp..aafrlsnppvlsvaalka.LelfdqaslealRkkSllLTdyleeLvkarlayklvleii 333
                                                +  e++   a +   ++p++s+a++++ Le+f+q+++  lR+kSl+LTd++++Lv++r+a    l++i
  FitnessBrowser__pseudo3_N2E3:AO353_05935 266 ASGYEPSSgiARYLCGTQPITSLAMVECgLEIFAQTDMPSLRRKSLALTDLFIQLVEQRCAA-HDLKLI 333
                                               6666666665889999*********************************************8.69**** PP

                                 TIGR01814 334 tPedtaer.sqlslkfskedkavlkalkkrdvviDkRePnviRlaPvpLYntfkDvykavevleeile 400
                                               tP+++a+r s++s++++ + +av++al++++v+ D+ReP ++R+  +pLY++f++v++av++l eil+
  FitnessBrowser__pseudo3_N2E3:AO353_05935 334 TPREHARRgSHVSFEHP-QGYAVIQALIAQGVIGDYREPRIMRFGFTPLYTSFTEVFDAVQILGEILD 400
                                               *****************.***********************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 nodes)
Target sequences:                          1  (416 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 29.77
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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 2024 update 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