Alignments for a candidate for kyn in Aquimarina agarilytica ZC1

GapMind for catabolism of small carbon sources

Alignments for a candidate for kyn in Aquimarina agarilytica ZC1

Align Kynureninase; L-kynurenine hydrolase; EC 3.7.1.3 (characterized)
to candidate WP_010179824.1 KQA_RS0207840 kynureninase

Query= SwissProt::Q9CXF0
         (464 letters)



>NCBI__GCF_000255455.1:WP_010179824.1
          Length = 425

 Score =  363 bits (932), Expect = e-105
 Identities = 192/429 (44%), Positives = 262/429 (61%), Gaps = 18/429 (4%)

Query: 33  LDEEDKLSHFRNCFYIPKMRDLPSIDLSLVSEDDDAIYFLGNSLGLQPKMVRTYLEEELD 92
           LD++D L+ +R+ F+ PK +              D IYF GNSLGLQPK+ RTY+EE L 
Sbjct: 13  LDKKDPLNQYRDQFHFPKHKG------------KDVIYFTGNSLGLQPKLARTYIEEILK 60

Query: 93  KWAKMGAYGHDVGKRPWIVGDESIVSLMKDIVGAHEKEIALMNALTINLHLLLLSFFKPT 152
            W  +G  GH   ++PW    E     +  +VGA  +E+ +MN LT+NLHLL++SF++PT
Sbjct: 61  DWETLGVEGHFEAEKPWWDYHERFGKQLSKVVGALPEEVTVMNTLTVNLHLLMVSFYRPT 120

Query: 153 PKRHKILLEAKAFPSDHYAIESQIQLHGLDVEKSMRMVKPREGEETLRMEDILEVIEEEG 212
            KR KI+ E KAFPSD Y I SQ++ HG D ++++  +K R GE   R ED+L+ I E G
Sbjct: 121 AKRFKIICEEKAFPSDQYMIASQVRFHGYDPKEAIVTLKKRTGEHNFRTEDVLKTIVEVG 180

Query: 213 DSIAVILFSGLHFYTGQLFNIPAITKAGHAKGCFVGFDLAHAVGNVELRLHDWGVDFACW 272
           +  A++L  G+++YTGQ+F++  ITKA   +G FVG+DLAHA GNV+L+LHDW VDFA W
Sbjct: 181 NECALVLIGGVNYYTGQVFDMETITKAAKDQGAFVGWDLAHAAGNVDLQLHDWDVDFAAW 240

Query: 273 CSYKYLNSGAGGLAGAFVHEK-HAHTVKPALVGWFGHDLSTRFNMDNKLQLIPGANGFRI 331
           CSYKY+NSG G  +G FVH+K H  T  P   GW+GH    RF M  +    P  N ++I
Sbjct: 241 CSYKYMNSGPGSASGCFVHKKHHGLTDIPRFEGWWGHHKKERFLMAPEFVPEPDVNAWQI 300

Query: 332 SNPPILLVCSLHASLEVFQQATMTALRRKSILLTGYLEYMLKHYHSKDNTENKGPIVNII 391
           SN P+L +    ASL++F    M A+  K  L+  YLE++L     K      G    II
Sbjct: 301 SNAPVLSMAPYLASLQLFDAVGMEAIITKRDLIVRYLEFILNSVSDK-----IGASFEII 355

Query: 392 TPSRAEERGCQLTLTFSIPKKSVFKELEKRGVVCDKREPDGIRVAPVPLYNSFHDVYKFI 451
           TPS  EERG QL++      K VF  L + GV  D REP+ IR+AP PLY S+ D++ F 
Sbjct: 356 TPSNPEERGTQLSVFLHGYGKKVFHYLMENGVFVDWREPNVIRLAPAPLYCSYTDMFNFG 415

Query: 452 RLLTSILDS 460
            +L   + S
Sbjct: 416 LILEQAIVS 424


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: 520
Number of extensions: 22
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: 425
Length adjustment: 32
Effective length of query: 432
Effective length of database: 393
Effective search space:   169776
Effective search space used:   169776
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 WP_010179824.1 KQA_RS0207840 (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.1301556.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.3e-132  427.6   0.0   2.7e-132  427.4   0.0    1.0  1  NCBI__GCF_000255455.1:WP_010179824.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000255455.1:WP_010179824.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  427.4   0.0  2.7e-132  2.7e-132       2     397 ..      11     420 ..      10     423 .. 0.96

  Alignments for each domain:
  == domain 1  score: 427.4 bits;  conditional E-value: 2.7e-132
                             TIGR01814   2 ealdaadelkalRdeFalpkakdeneviyldNSLalmpkaakealkeeldkWakllveshevgkapWleldea 74 
                                           + ld++d+l++ Rd+F++pk+k+++ +++ +NSL+l+pk a+++++e+l +W+ l ve+h+ +++pW +++e+
  NCBI__GCF_000255455.1:WP_010179824.1  11 KVLDKKDPLNQYRDQFHFPKHKGKDVIYFTGNSLGLQPKLARTYIEEILKDWETLGVEGHFEAEKPWWDYHER 83 
                                           789********************************************************************** PP

                             TIGR01814  75 leklla..lvakekevvvmnsltvNlhkllasfykptekRakIlleakaFPsDlyaiesqlklk.leveeslv 144
                                             k l+  ++a  +ev+vmn+ltvNlh+l++sfy+pt+kR+kI++e+kaFPsD y+i sq++ +  +++e +v
  NCBI__GCF_000255455.1:WP_010179824.1  84 FGKQLSkvVGALPEEVTVMNTLTVNLHLLMVSFYRPTAKRFKIICEEKAFPSDQYMIASQVRFHgYDPKEAIV 156
                                           9765555899*************************************************************** PP

                             TIGR01814 145 qvepre.eetlrledildviekeqdeiAlvllsgvqYkt.qlfdlaaitkaarkkgalvvfDLaHava.vple 214
                                           +++ r+ e+ +r+ed+l++i + ++e Alvl+ gv+Y+t q+fd+++itkaa+ +ga+v++DLaHa++ v+l+
  NCBI__GCF_000255455.1:WP_010179824.1 157 TLKKRTgEHNFRTEDVLKTIVEVGNECALVLIGGVNYYTgQVFDMETITKAAKDQGAFVGWDLAHAAGnVDLQ 229
                                           ******9****************************************************************** PP

                             TIGR01814 215 LhdwdvDfAvwCsYKylnasp.a.agafvhekka.keelprlalwwwhekskrfkmeeklelrp..aafrlsn 282
                                           LhdwdvDfA wCsYKy+n++p   +g+fvh+k+   ++ pr+ +ww+h+k+ rf m  +++++p  +a+++sn
  NCBI__GCF_000255455.1:WP_010179824.1 230 LHDWDVDFAAWCSYKYMNSGPgSaSGCFVHKKHHgLTDIPRFEGWWGHHKKERFLMAPEFVPEPdvNAWQISN 302
                                           *********************8579*****9986368889***********************999******* PP

                             TIGR01814 283 ppvlsvaalka.LelfdqaslealRkkSllLTdyleeLvkarlayk.lvleiitPedtaer.sqlslkfsked 352
                                            pvls+a+  a L+lfd + +ea+  k  l+  yle +++   ++   ++eiitP++ +er +qls+      
  NCBI__GCF_000255455.1:WP_010179824.1 303 APVLSMAPYLAsLQLFDAVGMEAIITKRDLIVRYLEFILNSVSDKIgASFEIITPSNPEERgTQLSVFLHGYG 375
                                           *******97777************999999999**99988877765799******************9999** PP

                             TIGR01814 353 kavlkalkkrdvviDkRePnviRlaPvpLYntfkDvykavevlee 397
                                           k+v+++l++++v +D+RePnviRlaP+pLY +++D++++  +le+
  NCBI__GCF_000255455.1:WP_010179824.1 376 KKVFHYLMENGVFVDWREPNVIRLAPAPLYCSYTDMFNFGLILEQ 420
                                           *************************************99877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 nodes)
Target sequences:                          1  (425 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 24.17
//
[ok]

This GapMind analysis is from Sep 24 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 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