Alignments for a candidate for kyn in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for kyn in Echinicola vietnamensis KMM 6221, DSM 17526

Align Kynureninase; L-kynurenine hydrolase; EC 3.7.1.3 (characterized)
to candidate Echvi_1449 Echvi_1449 kynureninase

Query= SwissProt::P70712
         (464 letters)



>FitnessBrowser__Cola:Echvi_1449
          Length = 426

 Score =  395 bits (1015), Expect = e-114
 Identities = 201/424 (47%), Positives = 273/424 (64%), Gaps = 23/424 (5%)

Query: 34  DEEDKLKRFKDCFYIPKMRDLPSIDLSLVNEDDNAIYFLGNSLGLQPKMVKTYLEEELDK 93
           D ED L++F+  F+ PK+              + AIYF GNSLGLQPK V+ +L+ +L+ 
Sbjct: 15  DREDPLRKFQSRFHFPKVNG------------EAAIYFCGNSLGLQPKAVREHLDRDLES 62

Query: 94  WAKIGAYGHEVGKRPWIIGDESIVSLMKDIVGAHEKEIALMNALTVNLHLLLLSFFKPTP 153
           WA     GH  G  PW    E   + + +IVGA + E+  M +LT NLH LL+SF++P  
Sbjct: 63  WASKAVDGHFEGDAPWFSVHERSKAALAEIVGAKKHEVVAMGSLTTNLHALLVSFYQPNG 122

Query: 154 KRHKILLEAKAFPSDHYAIESQIQLHGLDVEKSMRMIKPREGEETLRMEDILEVIEKEGD 213
           KR+KIL EA AFPSD YA+ESQ++ HGLD ++++  + PR GE T+R EDIL+ I K  D
Sbjct: 123 KRNKILTEAGAFPSDMYALESQVKYHGLDPDEAIVEVGPRPGEHTIRTEDILQAISKHQD 182

Query: 214 SIAVVLFSGLHFYTGQLFNIPAITQAGHAKGCFVGFDLAHAVGNVELHLHDWDVDFACWC 273
            +A V+ +GL +YTGQ+F++ AI  A HA G  VGFDLAHA GN  LHLHDW VDFA WC
Sbjct: 183 ELACVMMAGLQYYTGQVFDMKAIASAAHAVGATVGFDLAHAAGNAPLHLHDWGVDFAAWC 242

Query: 274 SYKYLNSGAGGLAGAFIHEKHAHTIKPAL---VGWFGHELSTRFNMDNKLQLIPGVNGFR 330
           SYKYLNSG G +AG F+HE+H +   PAL    GW+GH+   RF M+     + G +G++
Sbjct: 243 SYKYLNSGPGNVAGIFVHERHGN--NPALNRFAGWWGHDEKVRFKMEKGFVPMYGADGWQ 300

Query: 331 ISNPPILLVCSLHASLEIFQQATMTALRRKSILLTGYLEYLLKHYHGGNDTENKRPVVNI 390
            SN  +L + +  ASL+IFQ+A M  LR+KS+ LTG+L +L++   G      +  V+ +
Sbjct: 301 NSNGNVLGMAAHQASLDIFQEAGMVHLRKKSVQLTGFLAFLIREISG------ESGVLEV 354

Query: 391 ITPSRAEERGCQLTLTFSISKKGVFKELEKRGVVCDKREPEGIRVAPVPLYNSFHDVYKF 450
           ITP+   ERGCQL+L      K VF E  + G+V D R P  IR+AP PLYNSF DV++F
Sbjct: 355 ITPNAEAERGCQLSLLIHKGGKAVFDEFYQNGIVGDWRNPNVIRIAPTPLYNSFEDVFRF 414

Query: 451 IRLL 454
            ++L
Sbjct: 415 AKIL 418


Lambda     K      H
   0.321    0.139    0.419 

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: 551
Number of extensions: 26
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: 426
Length adjustment: 32
Effective length of query: 432
Effective length of database: 394
Effective search space:   170208
Effective search space used:   170208
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 Echvi_1449 Echvi_1449 (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.19274.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   2.2e-142  460.6   0.0   2.5e-142  460.4   0.0    1.0  1  lcl|FitnessBrowser__Cola:Echvi_1449  Echvi_1449 kynureninase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_1449  Echvi_1449 kynureninase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  460.4   0.0  2.5e-142  2.5e-142       1     399 [.      11     422 ..      11     423 .. 0.98

  Alignments for each domain:
  == domain 1  score: 460.4 bits;  conditional E-value: 2.5e-142
                            TIGR01814   1 aealdaadelkalRdeFalpkakdeneviyldNSLalmpkaakealkeeldkWakllveshevgkapWleldea 74 
                                          a+++d +d+l+++ ++F++pk+++e ++++ +NSL+l+pka++e l+  l++Wa  +v +h+ g+apW++++e+
  lcl|FitnessBrowser__Cola:Echvi_1449  11 AQERDREDPLRKFQSRFHFPKVNGEAAIYFCGNSLGLQPKAVREHLDRDLESWASKAVDGHFEGDAPWFSVHER 84 
                                          5899********************************************************************** PP

                            TIGR01814  75 leklla..lvakekevvvmnsltvNlhkllasfykptekRakIlleakaFPsDlyaiesqlklk.leveeslvq 145
                                           +  la  ++ak++evv+m slt Nlh ll+sfy+p  kR kIl+ea aFPsD+ya+esq+k + l+++e +v+
  lcl|FitnessBrowser__Cola:Echvi_1449  85 SKAALAeiVGAKKHEVVAMGSLTTNLHALLVSFYQPNGKRNKILTEAGAFPSDMYALESQVKYHgLDPDEAIVE 158
                                          9999888999**************************************************************** PP

                            TIGR01814 146 vepre.eetlrledildviekeqdeiAlvllsgvqYkt.qlfdlaaitkaarkkgalvvfDLaHava.vpleLh 216
                                          v pr  e+t+r+edil++i k+qde+A v++ g+qY+t q+fd++ai+ aa++ ga v+fDLaHa++  pl+Lh
  lcl|FitnessBrowser__Cola:Echvi_1449 159 VGPRPgEHTIRTEDILQAISKHQDELACVMMAGLQYYTgQVFDMKAIASAAHAVGATVGFDLAHAAGnAPLHLH 232
                                          *****9*************************************************************9****** PP

                            TIGR01814 217 dwdvDfAvwCsYKylnasp.a.agafvhekkake.elprlalwwwhekskrfkmeeklelrp..aafrlsnppv 285
                                          dw+vDfA wCsYKyln++p   ag+fvhe++ ++  l r+a+ww+h+++ rfkme+ +++     +++ sn +v
  lcl|FitnessBrowser__Cola:Echvi_1449 233 DWGVDFAAWCSYKYLNSGPgNvAGIFVHERHGNNpALNRFAGWWGHDEKVRFKMEKGFVPMYgaDGWQNSNGNV 306
                                          *******************8579********88725799*********************99889********* PP

                            TIGR01814 286 lsvaalka.LelfdqaslealRkkSllLTdyleeLvkarlayklvleiitPedtaer.sqlslkfskedkavlk 357
                                          l +aa +a L++f++a + +lRkkS++LT++l  L++    ++ vle+itP+ +aer +qlsl   k  kav+ 
  lcl|FitnessBrowser__Cola:Echvi_1449 307 LGMAAHQAsLDIFQEAGMVHLRKKSVQLTGFLAFLIREISGESGVLEVITPNAEAERgCQLSLLIHKGGKAVFD 380
                                          *******99***************************************************************** PP

                            TIGR01814 358 alkkrdvviDkRePnviRlaPvpLYntfkDvykavevleeil 399
                                          + +++++v D+R+PnviR+aP+pLYn+f+Dv+++ ++le+ l
  lcl|FitnessBrowser__Cola:Echvi_1449 381 EFYQNGIVGDWRNPNVIRIAPTPLYNSFEDVFRFAKILEQSL 422
                                          **************************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 nodes)
Target sequences:                          1  (426 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.33
//
[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