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

GapMind for catabolism of small carbon sources

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

Align Kynureninase (EC 3.7.1.3) (characterized)
to candidate PfGW456L13_4288 Kynureninase (EC 3.7.1.3)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_4288
         (416 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4288
          Length = 416

 Score =  840 bits (2169), Expect = 0.0
 Identities = 416/416 (100%), Positives = 416/416 (100%)

Query: 1   MTTRNDCLALDAQDALAPLRQQFALPEGVIYLDGNSLGARPVAALARAQAVIAEEWGNGL 60
           MTTRNDCLALDAQDALAPLRQQFALPEGVIYLDGNSLGARPVAALARAQAVIAEEWGNGL
Sbjct: 1   MTTRNDCLALDAQDALAPLRQQFALPEGVIYLDGNSLGARPVAALARAQAVIAEEWGNGL 60

Query: 61  IRSWNSAGWRDLPERLGNRLGGLIGAGDGEVVVTDTTSINLFKVLSAALRVQATRAPTRR 120
           IRSWNSAGWRDLPERLGNRLGGLIGAGDGEVVVTDTTSINLFKVLSAALRVQATRAPTRR
Sbjct: 61  IRSWNSAGWRDLPERLGNRLGGLIGAGDGEVVVTDTTSINLFKVLSAALRVQATRAPTRR 120

Query: 121 VIVTETGNFPTDLYIAEGLADMLQQGYTLRLVDSPQELPQAIDQDTAVVMLTHVNYKTGY 180
           VIVTETGNFPTDLYIAEGLADMLQQGYTLRLVDSPQELPQAIDQDTAVVMLTHVNYKTGY
Sbjct: 121 VIVTETGNFPTDLYIAEGLADMLQQGYTLRLVDSPQELPQAIDQDTAVVMLTHVNYKTGY 180

Query: 181 MHDMQALTTLTHECGALAIWDLAHSAGAVPVDLHQARADYAIGCTYKYLNGGPGSQAFVW 240
           MHDMQALTTLTHECGALAIWDLAHSAGAVPVDLHQARADYAIGCTYKYLNGGPGSQAFVW
Sbjct: 181 MHDMQALTTLTHECGALAIWDLAHSAGAVPVDLHQARADYAIGCTYKYLNGGPGSQAFVW 240

Query: 241 VSPELCDLVAQPLSGWFGHSRQFAMESHYQPSSGIARYLCGTQPITSLAMVECGLDVFAQ 300
           VSPELCDLVAQPLSGWFGHSRQFAMESHYQPSSGIARYLCGTQPITSLAMVECGLDVFAQ
Sbjct: 241 VSPELCDLVAQPLSGWFGHSRQFAMESHYQPSSGIARYLCGTQPITSLAMVECGLDVFAQ 300

Query: 301 TDMASLRSKSLALTDLFIQLVEQRCAAHELTLVTPREHAKRGSHVSFEHPQGYAVIQALI 360
           TDMASLRSKSLALTDLFIQLVEQRCAAHELTLVTPREHAKRGSHVSFEHPQGYAVIQALI
Sbjct: 301 TDMASLRSKSLALTDLFIQLVEQRCAAHELTLVTPREHAKRGSHVSFEHPQGYAVIQALI 360

Query: 361 ARGVIGDYREPRIMRFGFTPLYTSFTEVWDAVQILGDILDQKTWSQEQFQIRHSVT 416
           ARGVIGDYREPRIMRFGFTPLYTSFTEVWDAVQILGDILDQKTWSQEQFQIRHSVT
Sbjct: 361 ARGVIGDYREPRIMRFGFTPLYTSFTEVWDAVQILGDILDQKTWSQEQFQIRHSVT 416


Lambda     K      H
   0.321    0.135    0.412 

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: 728
Number of extensions: 16
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 PfGW456L13_4288 (Kynureninase (EC 3.7.1.3))
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.18089.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   7.7e-110  353.4   0.0   9.8e-110  353.1   0.0    1.1  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4288  Kynureninase (EC 3.7.1.3)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4288  Kynureninase (EC 3.7.1.3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  353.1   0.0  9.8e-110  9.8e-110       2     400 .]       8     400 ..       7     400 .. 0.91

  Alignments for each domain:
  == domain 1  score: 353.1 bits;  conditional E-value: 9.8e-110
                                               TIGR01814   2 ealdaadelkalRdeFalpkakdeneviyld.NSLalmp.kaakealkeeldkWa 54 
                                                              alda+d+l+ lR++Falp     + viyld NSL++ p +a+++a+  ++++W+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4288   8 LALDAQDALAPLRQQFALP-----EGVIYLDgNSLGARPvAALARAQAVIAEEWG 57 
                                                             78*****************.....99****66***9988356788999999**** PP

                                               TIGR01814  55 kllveshevgkapWleldealeklla..lvakekevvvmnsltvNlhkllasfyk 107
                                                             + l++s++  +a W +l+e+l + l   ++a + evvv++++++Nl+k+l+++++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4288  58 NGLIRSWN--SAGWRDLPERLGNRLGglIGAGDGEVVVTDTTSINLFKVLSAALR 110
                                                             ********..999********988877899*9*********************** PP

                                               TIGR01814 108 p....tekRakIlleakaFPsDlyaiesqlklkleveeslvqvepreeetlrled 158
                                                             +    +++R++I++e  +FP+Dly++e    +           +  +  tlrl d
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4288 111 VqatrAPTRRVIVTETGNFPTDLYIAEGLADML----------Q--QGYTLRLVD 153
                                                             9888899*******************9866665..........2..234677777 PP

                                               TIGR01814 159 ildvi.ekeqdeiAlvllsgvqYkt.qlfdlaaitkaarkkgalvvfDLaHava. 210
                                                              ++ + ++ +++ A+v+l++v+Ykt  + d++a+t++ ++ gal+++DLaH+++ 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4288 154 SPQELpQAIDQDTAVVMLTHVNYKTgYMHDMQALTTLTHECGALAIWDLAHSAGa 208
                                                             7665514456689************999*************************99 PP

                                               TIGR01814 211 vpleLhdwdvDfAvwCsYKylnaspaagafvhekkakeelprla..lwwwheksk 263
                                                             vp++Lh++ +D+A+ C+YKyln +p + afv+ ++   +l++++  +w++h +++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4288 209 VPVDLHQARADYAIGCTYKYLNGGPGSQAFVWVSPELCDLVAQPlsGWFGHSRQF 263
                                                             *************************999*******99999887622577777777 PP

                                               TIGR01814 264 rfkmeeklelrpaafrlsnppvlsvaalka.LelfdqaslealRkkSllLTdyle 317
                                                             +++++++ +   a +   ++p++s+a++++ L++f+q++++ lR+kSl+LTd+++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4288 264 AMESHYQPSSGIARYLCGTQPITSLAMVECgLDVFAQTDMASLRSKSLALTDLFI 318
                                                             777777666666999999************************************* PP

                                               TIGR01814 318 eLvkarlayklvleiitPedtaer.sqlslkfskedkavlkalkkrdvviDkReP 371
                                                             +Lv++r+a    l+++tP+++a+r s++s++++ + +av++al++r+v+ D+ReP
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4288 319 QLVEQRCAA-HELTLVTPREHAKRgSHVSFEHP-QGYAVIQALIARGVIGDYREP 371
                                                             ********8.79*********************.********************* PP

                                               TIGR01814 372 nviRlaPvpLYntfkDvykavevleeile 400
                                                              ++R+  +pLY++f++v++av++l +il+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4288 372 RIMRFGFTPLYTSFTEVWDAVQILGDILD 400
                                                             ************************99985 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 11.95
//
[ok]

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

Downloads

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

Related tools

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