Alignments for a candidate for kyn in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for kyn in Dyella japonica UNC79MFTsu3.2

Align Kynureninase; L-kynurenine hydrolase; EC 3.7.1.3 (characterized)
to candidate N515DRAFT_3776 N515DRAFT_3776 Kynureninase

Query= SwissProt::Q9CXF0
         (464 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3776
          Length = 428

 Score =  363 bits (932), Expect = e-105
 Identities = 192/421 (45%), Positives = 258/421 (61%), Gaps = 24/421 (5%)

Query: 34  DEEDKLSHFRNCFYIPKMRDLPSIDLSLVSEDDDAIYFLGNSLGLQPKMVRTYLEEELDK 93
           D  D L  FR+ F IP              +   + YF GNSLGLQP+ VR  L  ELD 
Sbjct: 16  DAADPLRAFRDEFLIPP------------HDGRASHYFCGNSLGLQPRAVREALTAELDD 63

Query: 94  WAKMGAYGHDVGKRPWIVGDESIVSLMKDIVGAHEKEIALMNALTINLHLLLLSFFKPTP 153
           W  +   GH  G++PW+   E +   + ++VGA   E+  MN L +NLHL+++SF++PTP
Sbjct: 64  WGALAVEGHFKGRQPWLDYHEYVRDDLAELVGALPSEVVAMNTLGVNLHLMMVSFYRPTP 123

Query: 154 KRHKILLEAKAFPSDHYAIESQIQLHGLDVEKSMRMVKPREGEETLRMEDILEVIEEEGD 213
            RH IL+EA AFP+D YA+ESQI+ HG     S+  ++P E   TL M  I   + E G+
Sbjct: 124 DRHAILIEAGAFPTDRYAVESQIRFHGFSPTLSLIELEPDEPNGTLSMGAIERALAEHGE 183

Query: 214 SIAVILFSGLHFYTGQLFNIPAITKAGHAKGCFVGFDLAHAVGNVELRLHDWGVDFACWC 273
            IA++L  G+ + TGQ F++ AIT   H +GC VGFDLAHAVGN+ LRLHD G DFA WC
Sbjct: 184 RIALVLLPGVQYRTGQAFDLKAITGLAHRQGCTVGFDLAHAVGNLPLRLHDSGADFAVWC 243

Query: 274 SYKYLNSGAGGLAGAFVHEKHAHTVK-PALVGWFGHDLSTRFNMDNKLQLIPGANGFRIS 332
           SYKYLNSG G +AGAFVH++HA T   P   GW+GHD  +RF M  +    PGA+G++IS
Sbjct: 244 SYKYLNSGPGAVAGAFVHDRHARTEHLPRFAGWWGHDKQSRFRMGPEFVPTPGADGWQIS 303

Query: 333 NPPILLVCSLHASLEVFQQATMTALRRKSILLTGYLEYMLKHYHSKDNTENKGPIVNIIT 392
           NPPIL +  L  SL++F +A M  LR KS+ LTGYLE++++             ++  +T
Sbjct: 304 NPPILSLAPLRVSLQIFHRAGMARLREKSLRLTGYLEWLVQ--------TQLADVLESVT 355

Query: 393 PSRAEERGCQLTLTFSIPK---KSVFKELEKRGVVCDKREPDGIRVAPVPLYNSFHDVYK 449
           P   E RG QL+L     +   +++F+ L + GVV D REPD IR++P PLYN F D   
Sbjct: 356 PRETERRGSQLSLRVLGGRERGRALFEYLMEHGVVGDWREPDVIRISPAPLYNRFEDCVG 415

Query: 450 F 450
           F
Sbjct: 416 F 416


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: 554
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: 428
Length adjustment: 32
Effective length of query: 432
Effective length of database: 396
Effective search space:   171072
Effective search space used:   171072
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 N515DRAFT_3776 N515DRAFT_3776 (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.10783.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   1.3e-144  467.9   0.0   1.5e-144  467.7   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_3776  N515DRAFT_3776 Kynureninase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_3776  N515DRAFT_3776 Kynureninase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  467.7   0.0  1.5e-144  1.5e-144       2     399 ..      13     424 ..      12     425 .. 0.97

  Alignments for each domain:
  == domain 1  score: 467.7 bits;  conditional E-value: 1.5e-144
                                    TIGR01814   2 ealdaadelkalRdeFalpkakdeneviyldNSLalmpkaakealkeeldkWakllveshevgkap 67 
                                                  +a daad+l+a+RdeF +p +++    ++ +NSL+l+p+a++eal +eld+W++l+ve+h+ g++p
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3776  13 RAQDAADPLRAFRDEFLIPPHDGRASHYFCGNSLGLQPRAVREALTAELDDWGALAVEGHFKGRQP 78 
                                                  678*************************************************************** PP

                                    TIGR01814  68 Wleldealeklla..lvakekevvvmnsltvNlhkllasfykptekRakIlleakaFPsDlyaies 131
                                                  Wl+++e++++ la  ++a  +evv+mn+l vNlh++++sfy+pt++R++Il+ea aFP+D+ya+es
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3776  79 WLDYHEYVRDDLAelVGALPSEVVAMNTLGVNLHLMMVSFYRPTPDRHAILIEAGAFPTDRYAVES 144
                                                  ********988777999************************************************* PP

                                    TIGR01814 132 qlklk.leveeslvqvepre.eetlrledildviekeqdeiAlvllsgvqYkt.qlfdlaaitkaa 194
                                                  q++ +  ++  sl+++ep+e ++tl++ +i+ ++++++++iAlvll+gvqY+t q+fdl+ait +a
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3776 145 QIRFHgFSPTLSLIELEPDEpNGTLSMGAIERALAEHGERIALVLLPGVQYRTgQAFDLKAITGLA 210
                                                  ****************************************************************** PP

                                    TIGR01814 195 rkkgalvvfDLaHava.vpleLhdwdvDfAvwCsYKylnasp.a.agafvhekkakee.lprlalw 256
                                                  +++g+ v+fDLaHav+ +pl+Lhd ++DfAvwCsYKyln++p a agafvh+++a++e lpr+a+w
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3776 211 HRQGCTVGFDLAHAVGnLPLRLHDSGADFAVWCSYKYLNSGPgAvAGAFVHDRHARTEhLPRFAGW 276
                                                  ******************************************877*********9765279***** PP

                                    TIGR01814 257 wwhekskrfkmeeklelrp..aafrlsnppvlsvaalka.LelfdqaslealRkkSllLTdyleeL 319
                                                  w+h+k++rf+m  +++++p   ++++snpp+ls+a+l+  L++f+ a ++ lR+kSl LT+yle L
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3776 277 WGHDKQSRFRMGPEFVPTPgaDGWQISNPPILSLAPLRVsLQIFHRAGMARLREKSLRLTGYLEWL 342
                                                  *******************999****************99************************** PP

                                    TIGR01814 320 vkarlayklvleiitPedtaer.sqlslkfs...kedkavlkalkkrdvviDkRePnviRlaPvpL 381
                                                  v+++la   vle +tP++t++r sqlsl++    +  +a++++l++++vv D+ReP+viR+ P+pL
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3776 343 VQTQLAD--VLESVTPRETERRgSQLSLRVLggrERGRALFEYLMEHGVVGDWREPDVIRISPAPL 406
                                                  ******6..9********************88878899**************************** PP

                                    TIGR01814 382 YntfkDvykavevleeil 399
                                                  Yn+f+D   + e+++ ++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3776 407 YNRFEDCVGFAEAVRAWA 424
                                                  *********999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 nodes)
Target sequences:                          1  (428 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 8.13
//
[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