Alignments for a candidate for kyn in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

GapMind for catabolism of small carbon sources

Alignments for a candidate for kyn in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align Kynureninase (EC 3.7.1.3) (characterized)
to candidate WP_068174000.1 HTA01S_RS17380 kynureninase

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



>NCBI__GCF_001592305.1:WP_068174000.1
          Length = 424

 Score =  484 bits (1245), Expect = e-141
 Identities = 250/425 (58%), Positives = 297/425 (69%), Gaps = 14/425 (3%)

Query: 5   TREQCLALDQEDPLRRLRDQFALPQGVIYLDGNSLGARPRSAAARAAEVVSEEWGTGLIR 64
           T++ C  LD  DPLR LR  F +P G IYLDGNSLG  P +A AR A+VV+ EWGT LI+
Sbjct: 3   TQQDCTTLDANDPLRDLRQLFNIPAGTIYLDGNSLGVMPAAAPARVADVVTREWGTDLIQ 62

Query: 65  SWNTAGWFELPQRLGNMLAPLIGAGEDEVVVTDTTSSNLFKVLAAALRVQQTRDPKRKVI 124
           SWN  GWF +PQ++G+ +A LIGAG  EVV TD+TS NLFKVL+AA+ +     P+RK I
Sbjct: 63  SWNKNGWFAMPQKVGDKIACLIGAGPGEVVATDSTSVNLFKVLSAAMNIAAADAPQRKRI 122

Query: 125 VSEASNFPTDLYIAQGLADLLQQGYSLRLVNAPEEIDAAVDADTAVLMLTHVNYKTGEML 184
           VSE SNFPTDLYIA+ L    Q G  L LV  PEEI A++ A+ A+LMLTHVNY+TG M 
Sbjct: 123 VSERSNFPTDLYIAEALCR--QHGMELVLVE-PEEIAASLTAEVAILMLTHVNYRTGAMH 179

Query: 185 DMASVTEMAHARGALTVWDLAHSAGAVPVALKASGADYAVGCTYKYLNGGPGSPAFLWVA 244
           DMA+VT  AHA G L VWDLAHSAGAVPV LK + AD+AVGC YKYLNGGPG+PAF+WV 
Sbjct: 180 DMAAVTAAAHAEGILAVWDLAHSAGAVPVDLKQAKADFAVGCGYKYLNGGPGAPAFVWVN 239

Query: 245 PSLRDAFWQPLSGWWGHAAPFAMEPGYRPREGVARFLCGTQPIASLAMVECGLDIY---- 300
           P   D FWQPL+GWWGHA PF   P YRP  G+ R+ C TQP+ SLA +ECG+D      
Sbjct: 240 PQHADRFWQPLAGWWGHATPFEFTPDYRPAPGITRYQCSTQPMISLAALECGVDTVLAAE 299

Query: 301 AQTDMAVLRAKSLMLTDLFIALVETRCAAHPLELVTPRAHARRGSHVSFAHPDG-FAVVQ 359
           A   MA LRAKSL LTDLFI LVE RC  + L L TPR HA+RGS V     +G +A+VQ
Sbjct: 300 AHGGMAALRAKSLALTDLFIQLVEERCEGNGLGLATPREHAQRGSQVCLTRDEGAYAIVQ 359

Query: 360 ALIERGVIGDY------REPRIARFGFTPLYTSFTEVWDAVEILRDVLDSGTYKAERHQT 413
           ALI RGVIGDY      R   I RFGFTPLY  F +VW+AVE L+ VL++G ++      
Sbjct: 360 ALIARGVIGDYRAGDGGRHKDILRFGFTPLYIGFADVWNAVEQLKQVLETGEWQRPEFNR 419

Query: 414 RGLVT 418
           +  VT
Sbjct: 420 KHAVT 424


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: 580
Number of extensions: 26
Number of successful extensions: 5
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: 424
Length adjustment: 32
Effective length of query: 386
Effective length of database: 392
Effective search space:   151312
Effective search space used:   151312
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_068174000.1 HTA01S_RS17380 (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.3374659.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.1e-100  323.3   0.0   1.3e-100  323.0   0.0    1.0  1  NCBI__GCF_001592305.1:WP_068174000.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001592305.1:WP_068174000.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  323.0   0.0  1.3e-100  1.3e-100       2     400 .]       8     408 ..       7     408 .. 0.91

  Alignments for each domain:
  == domain 1  score: 323.0 bits;  conditional E-value: 1.3e-100
                             TIGR01814   2 ealdaadelkalRdeFalpkakdeneviyld.NSLalmpkaakeal.keeldkWakllveshevgkapWleld 72 
                                            +lda+d+l++lR+ F++p       +iyld NSL++mp+aa + + + ++ +W+  l++s++  k  W+ ++
  NCBI__GCF_001592305.1:WP_068174000.1   8 TTLDANDPLRDLRQLFNIP-----AGTIYLDgNSLGVMPAAAPARVaDVVTREWGTDLIQSWN--KNGWFAMP 73 
                                           689****************.....89999966********9976551567789**********..999***** PP

                             TIGR01814  73 ealeklla..lvakekevvvmnsltvNlhkllasfykp....tekRakIlleakaFPsDlyaiesqlklklev 139
                                           +++ +  a  ++a   evv+++s++vNl+k+l+++++     +++R+ I++e ++FP+Dly++e+ ++ +   
  NCBI__GCF_001592305.1:WP_068174000.1  74 QKVGDKIAclIGAGPGEVVATDSTSVNLFKVLSAAMNIaaadAPQRKRIVSERSNFPTDLYIAEALCRQH--- 143
                                           ***988888999***********************998778899**************************... PP

                             TIGR01814 140 eeslvqvepreeetlrledildviekeqdeiAlvllsgvqYkt.qlfdlaaitkaarkkgalvvfDLaHava. 210
                                              lv vep+e           + +  + e+A+ +l++v+Y+t  + d+aa+t+aa+++g l+v+DLaH+++ 
  NCBI__GCF_001592305.1:WP_068174000.1 144 GMELVLVEPEE-----------IAASLTAEVAILMLTHVNYRTgAMHDMAAVTAAAHAEGILAVWDLAHSAGa 205
                                           77899999999...........44445567*************99**************************99 PP

                             TIGR01814 211 vpleLhdwdvDfAvwCsYKylnaspaagafvhekkakeelprla..lwwwhekskrfkmeeklelrpaafrls 281
                                           vp++L ++++DfAv C YKyln +p a afv+ ++ ++++++++  +ww+h+++++f+ +++ ++  + ++ s
  NCBI__GCF_001592305.1:WP_068174000.1 206 VPVDLKQAKADFAVGCGYKYLNGGPGAPAFVWVNPQHADRFWQPlaGWWGHATPFEFTPDYRPAPGITRYQCS 278
                                           *************************999*************975337**************999888****** PP

                             TIGR01814 282 nppvlsvaalka.Lelf..dqa..slealRkkSllLTdyleeLvkarlayklvleiitPedtaer.sqlslkf 348
                                           ++p++s+aal++  +    ++a   ++alR+kSl+LTd++++Lv+ r++    l ++tP+++a+r sq+ l+ 
  NCBI__GCF_001592305.1:WP_068174000.1 279 TQPMISLAALECgVDTVlaAEAhgGMAALRAKSLALTDLFIQLVEERCEG-NGLGLATPREHAQRgSQVCLTR 350
                                           *************885522333336************************8.69******************** PP

                             TIGR01814 349 skedkavlkalkkrdvviDkReP......nviRlaPvpLYntfkDvykavevleeile 400
                                           ++ ++a+++al++r+v+ D+R+       +++R+  +pLY  f Dv++ave l+++le
  NCBI__GCF_001592305.1:WP_068174000.1 351 DEGAYAIVQALIARGVIGDYRAGdggrhkDILRFGFTPLYIGFADVWNAVEQLKQVLE 408
                                           ********************87522222279***********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 nodes)
Target sequences:                          1  (424 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 26.50
//
[ok]

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

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Protein sequences (fasta format)
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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