Alignments for a candidate for kyn in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for kyn in Cupriavidus basilensis 4G11

Align Kynureninase (EC 3.7.1.3) (characterized)
to candidate RR42_RS15385 RR42_RS15385 kynureninase

Query= reanno::Cup4G11:RR42_RS15385
         (418 letters)



>FitnessBrowser__Cup4G11:RR42_RS15385
          Length = 418

 Score =  839 bits (2167), Expect = 0.0
 Identities = 418/418 (100%), Positives = 418/418 (100%)

Query: 1   MTAMTREQCLALDQEDPLRRLRDQFALPQGVIYLDGNSLGARPRSAAARAAEVVSEEWGT 60
           MTAMTREQCLALDQEDPLRRLRDQFALPQGVIYLDGNSLGARPRSAAARAAEVVSEEWGT
Sbjct: 1   MTAMTREQCLALDQEDPLRRLRDQFALPQGVIYLDGNSLGARPRSAAARAAEVVSEEWGT 60

Query: 61  GLIRSWNTAGWFELPQRLGNMLAPLIGAGEDEVVVTDTTSSNLFKVLAAALRVQQTRDPK 120
           GLIRSWNTAGWFELPQRLGNMLAPLIGAGEDEVVVTDTTSSNLFKVLAAALRVQQTRDPK
Sbjct: 61  GLIRSWNTAGWFELPQRLGNMLAPLIGAGEDEVVVTDTTSSNLFKVLAAALRVQQTRDPK 120

Query: 121 RKVIVSEASNFPTDLYIAQGLADLLQQGYSLRLVNAPEEIDAAVDADTAVLMLTHVNYKT 180
           RKVIVSEASNFPTDLYIAQGLADLLQQGYSLRLVNAPEEIDAAVDADTAVLMLTHVNYKT
Sbjct: 121 RKVIVSEASNFPTDLYIAQGLADLLQQGYSLRLVNAPEEIDAAVDADTAVLMLTHVNYKT 180

Query: 181 GEMLDMASVTEMAHARGALTVWDLAHSAGAVPVALKASGADYAVGCTYKYLNGGPGSPAF 240
           GEMLDMASVTEMAHARGALTVWDLAHSAGAVPVALKASGADYAVGCTYKYLNGGPGSPAF
Sbjct: 181 GEMLDMASVTEMAHARGALTVWDLAHSAGAVPVALKASGADYAVGCTYKYLNGGPGSPAF 240

Query: 241 LWVAPSLRDAFWQPLSGWWGHAAPFAMEPGYRPREGVARFLCGTQPIASLAMVECGLDIY 300
           LWVAPSLRDAFWQPLSGWWGHAAPFAMEPGYRPREGVARFLCGTQPIASLAMVECGLDIY
Sbjct: 241 LWVAPSLRDAFWQPLSGWWGHAAPFAMEPGYRPREGVARFLCGTQPIASLAMVECGLDIY 300

Query: 301 AQTDMAVLRAKSLMLTDLFIALVETRCAAHPLELVTPRAHARRGSHVSFAHPDGFAVVQA 360
           AQTDMAVLRAKSLMLTDLFIALVETRCAAHPLELVTPRAHARRGSHVSFAHPDGFAVVQA
Sbjct: 301 AQTDMAVLRAKSLMLTDLFIALVETRCAAHPLELVTPRAHARRGSHVSFAHPDGFAVVQA 360

Query: 361 LIERGVIGDYREPRIARFGFTPLYTSFTEVWDAVEILRDVLDSGTYKAERHQTRGLVT 418
           LIERGVIGDYREPRIARFGFTPLYTSFTEVWDAVEILRDVLDSGTYKAERHQTRGLVT
Sbjct: 361 LIERGVIGDYREPRIARFGFTPLYTSFTEVWDAVEILRDVLDSGTYKAERHQTRGLVT 418


Lambda     K      H
   0.321    0.135    0.410 

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: 775
Number of extensions: 21
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: 418
Length of database: 418
Length adjustment: 32
Effective length of query: 386
Effective length of database: 386
Effective search space:   148996
Effective search space used:   148996
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 RR42_RS15385 RR42_RS15385 (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.4943.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-110  355.8   0.0   1.9e-110  355.4   0.0    1.1  1  lcl|FitnessBrowser__Cup4G11:RR42_RS15385  RR42_RS15385 kynureninase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS15385  RR42_RS15385 kynureninase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  355.4   0.0  1.9e-110  1.9e-110       2     400 .]      10     402 ..       9     402 .. 0.91

  Alignments for each domain:
  == domain 1  score: 355.4 bits;  conditional E-value: 1.9e-110
                                 TIGR01814   2 ealdaadelkalRdeFalpkakdeneviyld.NSLalmpkaak.ealkeeldkWakllveshevgkapW 68 
                                                ald++d+l++lRd+Falp     + viyld NSL++ p++a+ +a + + ++W+  l++s++  +a W
  lcl|FitnessBrowser__Cup4G11:RR42_RS15385  10 LALDQEDPLRRLRDQFALP-----QGVIYLDgNSLGARPRSAAaRAAEVVSEEWGTGLIRSWN--TAGW 71 
                                               78*****************.....89****66*******98761566777899**********..99** PP

                                 TIGR01814  69 leldealeklla..lvakekevvvmnsltvNlhkllasfykp....tekRakIlleakaFPsDlyaies 131
                                               +el+++l ++la  ++a e+evvv+++++ Nl+k+la+++++     +kR++I++ea++FP+Dly+++ 
  lcl|FitnessBrowser__Cup4G11:RR42_RS15385  72 FELPQRLGNMLAplIGAGEDEVVVTDTTSSNLFKVLAAALRVqqtrDPKRKVIVSEASNFPTDLYIAQG 140
                                               ***********99999*************************97777799*****************998 PP

                                 TIGR01814 132 qlklkleveeslvqvepreeetlrledildviekeqd.eiAlvllsgvqYkt.qlfdlaaitkaarkkg 198
                                                  l  ++              lrl ++++ i+++ d + A+ +l++v+Ykt +++d+a +t+ a+++g
  lcl|FitnessBrowser__Cup4G11:RR42_RS15385 141 LADLL-QQG-----------YSLRLVNAPEEIDAAVDaDTAVLMLTHVNYKTgEMLDMASVTEMAHARG 197
                                               77776.222...........35677777777776654389***************************** PP

                                 TIGR01814 199 alvvfDLaHava.vpleLhdwdvDfAvwCsYKylnaspaagafvhekkakeelprla..lwwwhekskr 264
                                               al v+DLaH+++ vp+ L + ++D+Av C+YKyln +p + af++ ++  ++ ++++  +ww+h+ +++
  lcl|FitnessBrowser__Cup4G11:RR42_RS15385 198 ALTVWDLAHSAGaVPVALKASGADYAVGCTYKYLNGGPGSPAFLWVAPSLRDAFWQPlsGWWGHAAPFA 266
                                               ***********99*************************999************9986337999999988 PP

                                 TIGR01814 265 fkmeeklelrpaafrlsnppvlsvaalka.LelfdqaslealRkkSllLTdyleeLvkarlayklvlei 332
                                               ++  ++     a f   ++p+ s+a++++ L++++q++++ lR+kSl+LTd+++ Lv++r+a    le+
  lcl|FitnessBrowser__Cup4G11:RR42_RS15385 267 MEPGYRPREGVARFLCGTQPIASLAMVECgLDIYAQTDMAVLRAKSLMLTDLFIALVETRCAA-HPLEL 334
                                               77777555555778888*********************************************8.69*** PP

                                 TIGR01814 333 itPedtaer.sqlslkfskedkavlkalkkrdvviDkRePnviRlaPvpLYntfkDvykavevleeile 400
                                               +tP+ +a+r s++s++++ + +av++al++r+v+ D+ReP + R+  +pLY++f++v++ave+l+++l+
  lcl|FitnessBrowser__Cup4G11:RR42_RS15385 335 VTPRAHARRgSHVSFAHP-DGFAVVQALIERGVIGDYREPRIARFGFTPLYTSFTEVWDAVEILRDVLD 402
                                               ******************.***********************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 nodes)
Target sequences:                          1  (418 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: 10.36
//
[ok]

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

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Steps (tab-delimited)
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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 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