Alignments for a candidate for kyn in Pedobacter sp. GW460-11-11-14-LB5

GapMind for catabolism of small carbon sources

Alignments for a candidate for kyn in Pedobacter sp. GW460-11-11-14-LB5

Align Kynureninase; L-kynurenine hydrolase; EC 3.7.1.3 (characterized)
to candidate CA265_RS09295 CA265_RS09295 kynureninase

Query= SwissProt::Q9CXF0
         (464 letters)



>FitnessBrowser__Pedo557:CA265_RS09295
          Length = 429

 Score =  360 bits (923), Expect = e-104
 Identities = 193/417 (46%), Positives = 259/417 (62%), Gaps = 18/417 (4%)

Query: 34  DEEDKLSHFRNCFYIPKMRDLPSIDLSLVSEDDDAIYFLGNSLGLQPKMVRTYLEEELDK 93
           DE D+L  FR+ F  P                 D IY  GNSLGLQPK+    L+ +L+ 
Sbjct: 14  DETDQLRDFRSQFLFPN------------HNGKDLIYLCGNSLGLQPKVAGEVLKNQLNN 61

Query: 94  WAKMGAYGHDVGKRPWIVGDESIVSLMKDIVGAHEKEIALMNALTINLHLLLLSFFKPTP 153
           WA     G   G  PWI   +++  LM  IVGA   E+  MN LT+NLHLL++SF++P  
Sbjct: 62  WANYAVEGWFDGNEPWIFYHKALKKLMAPIVGALPSEVCPMNTLTVNLHLLMVSFYQPKG 121

Query: 154 KRHKILLEAKAFPSDHYAIESQIQLHGLDVEKSMRMVKPREGEETLRMEDILEVIEEEGD 213
           KR KI++E  AFPSD YAIESQ++ HG D ++++  V P+EGEE L   DI+  I+E  D
Sbjct: 122 KRFKIIMEGGAFPSDQYAIESQVRFHGFDPKEAIIEVFPKEGEEILHTADIIAQIKENAD 181

Query: 214 SIAVILFSGLHFYTGQLFNIPAITKAGHAKGCFVGFDLAHAVGNVELRLHDWGVDFACWC 273
            IA++LF G+++YTGQ +++  ITKAGH  G  VG+DLAHA GNV ++LHDW VDFACWC
Sbjct: 182 EIALVLFGGINYYTGQWYDMETITKAGHEIGAIVGWDLAHAAGNVPVKLHDWDVDFACWC 241

Query: 274 SYKYLNSGAGGLAGAFVHEKH-AHTVKPALVGWFGHDLSTRFNMDNKLQLIPGANGFRIS 332
           SYKY NSG GG++G FVHEKH  +T      GW+G+    RF M+       GA+G+++S
Sbjct: 242 SYKYQNSGPGGISGIFVHEKHFNNTGLNRFAGWWGYQEHKRFKMEKGFIPETGADGWQVS 301

Query: 333 NPPILLVCSLHASLEVFQQA-TMTALRRKSILLTGYLEYMLKHYHSKDNTENKGPIVNII 391
              ++ +   HASL++F+QA  +  LR KSI LT YLEY++    ++ N E       II
Sbjct: 302 CTQVMPMALYHASLQIFEQAGFIEPLRNKSITLTAYLEYII----NEINKELGVLQYKII 357

Query: 392 TPSRAEERGCQLTLTFSIPKKSVFKELEKRGVVCDKREPDGIRVAPVPLYNSFHDVY 448
           TP  A++RG QL++      K +F  L    V+ D REPD IR++ VPLYNSF DVY
Sbjct: 358 TPKVAKDRGAQLSIIAERNGKQIFDGLMANHVLGDWREPDVIRLSAVPLYNSFEDVY 414


Lambda     K      H
   0.321    0.139    0.417 

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: 506
Number of extensions: 23
Number of successful extensions: 4
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: 464
Length of database: 429
Length adjustment: 33
Effective length of query: 431
Effective length of database: 396
Effective search space:   170676
Effective search space used:   170676
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 (21.8 bits)
S2: 51 (24.3 bits)

Align candidate CA265_RS09295 CA265_RS09295 (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.19433.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   4.8e-132  426.5   0.0   5.7e-132  426.3   0.0    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS09295  CA265_RS09295 kynureninase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS09295  CA265_RS09295 kynureninase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  426.3   0.0  5.7e-132  5.7e-132       2     396 ..      11     421 ..      10     425 .. 0.95

  Alignments for each domain:
  == domain 1  score: 426.3 bits;  conditional E-value: 5.7e-132
                                  TIGR01814   2 ealdaadelkalRdeFalpkakdeneviyld.NSLalmpkaakealkeeldkWakllveshevgkapW 68 
                                                ++ d+ d+l+++R++F +p+++++ + iyl+ NSL+l+pk+a e+lk++l++Wa+++ve+++ g+ pW
  lcl|FitnessBrowser__Pedo557:CA265_RS09295  11 QTQDETDQLRDFRSQFLFPNHNGK-DLIYLCgNSLGLQPKVAGEVLKNQLNNWANYAVEGWFDGNEPW 77 
                                                6789***************76665.5666644************************************ PP

                                  TIGR01814  69 leldealeklla..lvakekevvvmnsltvNlhkllasfykptekRakIlleakaFPsDlyaiesqlk 134
                                                + +++al+kl+a  ++a  +ev  mn+ltvNlh+l++sfy+p  kR+kI++e  aFPsD yaiesq++
  lcl|FitnessBrowser__Pedo557:CA265_RS09295  78 IFYHKALKKLMApiVGALPSEVCPMNTLTVNLHLLMVSFYQPKGKRFKIIMEGGAFPSDQYAIESQVR 145
                                                *************999**************************************************** PP

                                  TIGR01814 135 lk.leveeslvqvepre.eetlrledildviekeqdeiAlvllsgvqYkt.qlfdlaaitkaarkkga 199
                                                 +  +++e +++v p+e ee l++ di + i+++ deiAlvl+ g++Y+t q +d+++itka+++ ga
  lcl|FitnessBrowser__Pedo557:CA265_RS09295 146 FHgFDPKEAIIEVFPKEgEEILHTADIIAQIKENADEIALVLFGGINYYTgQWYDMETITKAGHEIGA 213
                                                ******************************************************************** PP

                                  TIGR01814 200 lvvfDLaHava.vpleLhdwdvDfAvwCsYKylnasp.a.agafvhekkakee.lprlalwwwheksk 263
                                                +v++DLaHa++ vp++LhdwdvDfA+wCsYKy n++p   +g+fvhek+++++ l r+a+ww+ ++ k
  lcl|FitnessBrowser__Pedo557:CA265_RS09295 214 IVGWDLAHAAGnVPVKLHDWDVDFACWCSYKYQNSGPgGiSGIFVHEKHFNNTgLNRFAGWWGYQEHK 281
                                                *************************************856*********9765389************ PP

                                  TIGR01814 264 rfkmeeklelrp..aafrlsnppvlsvaalka.Lelfdqas.lealRkkSllLTdyleeLvkarlayk 327
                                                rfkme+ + ++    ++++s  +v+ +a  +a L++f+qa  +e lR+kS++LT yle++++   ++ 
  lcl|FitnessBrowser__Pedo557:CA265_RS09295 282 RFKMEKGFIPETgaDGWQVSCTQVMPMALYHAsLQIFEQAGfIEPLRNKSITLTAYLEYIINEINKEL 349
                                                *********999989****************99******985799****************8766655 PP

                                  TIGR01814 328 ..lvleiitPedtaer.sqlslkfskedkavlkalkkrdvviDkRePnviRlaPvpLYntfkDvykav 392
                                                  l  +iitP+  ++r +qls+  + + k+++  l++++v+ D+ReP+viRl  vpLYn+f+Dvy a 
  lcl|FitnessBrowser__Pedo557:CA265_RS09295 350 gvLQYKIITPKVAKDRgAQLSIIAERNGKQIFDGLMANHVLGDWREPDVIRLSAVPLYNSFEDVYLAG 417
                                                556678***********************************************************988 PP

                                  TIGR01814 393 evle 396
                                                ++l 
  lcl|FitnessBrowser__Pedo557:CA265_RS09295 418 QALL 421
                                                8775 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 nodes)
Target sequences:                          1  (429 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: 11.63
//
[ok]

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

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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