Alignments for a candidate for kyn in Rhizorhabdus wittichii RW1

GapMind for catabolism of small carbon sources

Alignments for a candidate for kyn in Rhizorhabdus wittichii RW1

Align Kynureninase (EC 3.7.1.3) (characterized)
to candidate WP_011951526.1 SWIT_RS03465 kynureninase

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



>NCBI__GCF_000016765.1:WP_011951526.1
          Length = 413

 Score =  448 bits (1153), Expect = e-130
 Identities = 236/416 (56%), Positives = 283/416 (68%), Gaps = 6/416 (1%)

Query: 3   AMTREQCLALDQEDPLRRLRDQFALPQGVIYLDGNSLGARPRSAAARAAEVVSEEWGTGL 62
           A+ RE   ALD  DPLR  R  FALP GVIYL+GNSLGA P SAAAR   +V +EW   L
Sbjct: 4   ALDREAARALDAADPLRGKRAGFALPDGVIYLNGNSLGAAPLSAAARVGRLVRDEWARDL 63

Query: 63  IRSWNTAGWFELPQRLGNMLAPLIGAGEDEVVVTDTTSSNLFKVLAAALRVQQTRDPKRK 122
           I SWN   W   PQRLG  +A LIGA  DEV + D+TS NL+K+L AA     T  P RK
Sbjct: 64  IGSWNVHDWIGAPQRLGARIARLIGAEADEVAIADSTSVNLYKLLVAAC----TARPGRK 119

Query: 123 VIVSEASNFPTDLYIAQGLADLLQQGYSLRLVNAPEEIDAAVDADTAVLMLTHVNYKTGE 182
            I+SE  NFPTDLYIAQG+A  L    ++R V      DA +DADTAV++LTHV+YK+G 
Sbjct: 120 TILSEPGNFPTDLYIAQGVAATLGDR-TVRTVEIDRLCDA-IDADTAVVLLTHVHYKSGH 177

Query: 183 MLDMASVTEMAHARGALTVWDLAHSAGAVPVALKASGADYAVGCTYKYLNGGPGSPAFLW 242
           MLDMA++T  AHA+GAL +WDL+HS GA+PV L    AD AVGC YKYLNGGPG+PAFL+
Sbjct: 178 MLDMAAITAAAHAQGALVLWDLSHSVGALPVDLNGCAADLAVGCGYKYLNGGPGAPAFLY 237

Query: 243 VAPSLRDAFWQPLSGWWGHAAPFAMEPGYRPREGVARFLCGTQPIASLAMVECGLDIYAQ 302
           VA  L+     PL+GW GH APFA    Y P  G+ARFLCGT PI ++A +E GL  +  
Sbjct: 238 VARRLQAELVSPLTGWMGHDAPFAFGDDYVPATGIARFLCGTPPILAMAALEEGLAQFDD 297

Query: 303 TDMAVLRAKSLMLTDLFIALVETRCAAHPLELVTPRAHARRGSHVSFAHPDGFAVVQALI 362
                +  KS  L D FIA+VE RCA H LEL++PR  ARRGSHVSFAHPD +A+ QALI
Sbjct: 298 VSFDDILTKSRTLGDHFIAMVEARCAGHDLELISPRDAARRGSHVSFAHPDAYALCQALI 357

Query: 363 ERGVIGDYREPRIARFGFTPLYTSFTEVWDAVEILRDVLDSGTYKAERHQTRGLVT 418
            RGV+GD+R P   RFGFTPLYTSF ++W+AVEIL  VLD   +    ++ R  VT
Sbjct: 358 ARGVVGDFRAPDAIRFGFTPLYTSFEDIWNAVEILERVLDERAWDRSEYRVRAAVT 413


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: 533
Number of extensions: 20
Number of successful extensions: 3
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: 413
Length adjustment: 31
Effective length of query: 387
Effective length of database: 382
Effective search space:   147834
Effective search space used:   147834
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 WP_011951526.1 SWIT_RS03465 (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.3259281.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    3.8e-96  308.3   0.0    6.5e-96  307.6   0.0    1.3  1  NCBI__GCF_000016765.1:WP_011951526.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000016765.1:WP_011951526.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  307.6   0.0   6.5e-96   6.5e-96       2     400 .]      11     397 ..      10     397 .. 0.92

  Alignments for each domain:
  == domain 1  score: 307.6 bits;  conditional E-value: 6.5e-96
                             TIGR01814   2 ealdaadelkalRdeFalpkakdeneviyl.dNSLalmpkaakeal.keeldkWakllveshevgkapWleld 72 
                                           +aldaad+l+  R  Falp     + viyl +NSL+++p +a++ + + + d+Wa+ l+ s++   ++W+  +
  NCBI__GCF_000016765.1:WP_011951526.1  11 RALDAADPLRGKRAGFALP-----DGVIYLnGNSLGAAPLSAAARVgRLVRDEWARDLIGSWN--VHDWIGAP 76 
                                           79*****************.....99999966*******887766615677************..899***** PP

                             TIGR01814  73 ealeklla..lvakekevvvmnsltvNlhkllasfykptekRakIlleakaFPsDlyaies.qlklklevees 142
                                           ++l    a  ++a+++ev++++s++vNl+kll+++    + R+ Il+e  +FP+Dly+++  + +l       
  NCBI__GCF_000016765.1:WP_011951526.1  77 QRLGARIArlIGAEADEVAIADSTSVNLYKLLVAACTARPGRKTILSEPGNFPTDLYIAQGvAATLG------ 143
                                           ***988777899*********************************************9975134444...... PP

                             TIGR01814 143 lvqvepreeetlrledildviekeqdeiAlvllsgvqYkt.qlfdlaaitkaarkkgalvvfDLaHava.vpl 213
                                                   + t+r+ +i  + ++ + + A+vll++v+Yk+ +++d+aait+aa+++galv +DL+H+v+ +p+
  NCBI__GCF_000016765.1:WP_011951526.1 144 --------DRTVRTVEIDRLCDAIDADTAVVLLTHVHYKSgHMLDMAAITAAAHAQGALVLWDLSHSVGaLPV 208
                                           ........56899999999****************************************************** PP

                             TIGR01814 214 eLhdwdvDfAvwCsYKylnaspaagafvh..ekkakeelprlalwwwhekskrfkmeeklelrpaafrlsnpp 284
                                           +L+   +D Av C YKyln +p a af++   +   e    l++w +h+ +++f  ++  ++  a f   +pp
  NCBI__GCF_000016765.1:WP_011951526.1 209 DLNGCAADLAVGCGYKYLNGGPGAPAFLYvaRRLQAELVSPLTGWMGHDAPFAFGDDYVPATGIARFLCGTPP 281
                                           **********************6666665103444444456899**************877777888899*** PP

                             TIGR01814 285 vlsvaalka.LelfdqaslealRkkSllLTdyleeLvkarlayklvleiitPedtaer.sqlslkfskedkav 355
                                           +l++aal+  L  fd++s +++  kS +L d+++ +v+ar+a    le+i+P+d a+r s++s++++ +++a+
  NCBI__GCF_000016765.1:WP_011951526.1 282 ILAMAALEEgLAQFDDVSFDDILTKSRTLGDHFIAMVEARCAG-HDLELISPRDAARRgSHVSFAHP-DAYAL 352
                                           ********99********************************7.69*********************.***** PP

                             TIGR01814 356 lkalkkrdvviDkRePnviRlaPvpLYntfkDvykavevleeile 400
                                           ++al++r+vv D+R+P+ iR+  +pLY++f+D+++ave+le +l+
  NCBI__GCF_000016765.1:WP_011951526.1 353 CQALIARGVVGDFRAPDAIRFGFTPLYTSFEDIWNAVEILERVLD 397
                                           *****************************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 nodes)
Target sequences:                          1  (413 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: 00:00:00.02
# Mc/sec: 6.81
//
[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