Alignments for a candidate for kyn in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for kyn in Burkholderia phytofirmans PsJN

Align Kynureninase (EC 3.7.1.3) (characterized)
to candidate BPHYT_RS07275 BPHYT_RS07275 kynureninase

Query= reanno::WCS417:GFF4622
         (416 letters)



>FitnessBrowser__BFirm:BPHYT_RS07275
          Length = 409

 Score =  429 bits (1104), Expect = e-125
 Identities = 218/416 (52%), Positives = 278/416 (66%), Gaps = 7/416 (1%)

Query: 1   MTTRSHCQALDAQDPLAPLRSQFALPEGVIYLDGNSLGARPVAALARAQAVIAEEWGNGL 60
           M TR HC ALDA D LA  R++F LP   IYLDGNSLGA P    AR +  +  EW +GL
Sbjct: 1   MITREHCAALDAADTLAHCRARFDLPADTIYLDGNSLGAMPANVPARIEQALKHEWAHGL 60

Query: 61  IRSWNNAGWADLSLRLGNRLAPLIGARDNEVAITDTTSINLFKVLSAALTVQRQRQPGRK 120
           IRSWN+AGW     R GN++A LIGA  +EV + D+TS+NLFKVL AA  ++    PGR 
Sbjct: 61  IRSWNDAGWYPAPQRTGNKIARLIGAGQDEVIVADSTSVNLFKVLVAATRMR----PGRN 116

Query: 121 VIVSEASNFPTDLYIAEGLAELLQQGYSLRLVNSPDELPQAIDQDVAVVMLTHVNYKTGY 180
           VI++E +NFPTD+YIA  +AE+   G  LR V+ PDE+  AID  VA+V LTHVNYKTG 
Sbjct: 117 VILAERTNFPTDVYIASSVAEMT--GCDLRCVD-PDEIVSAIDDTVAIVSLTHVNYKTGK 173

Query: 181 MYDMQALTALSHECGALSIWDLAHSAGAVPIDLHQAGADYAIGCTYKYLNGGPGSQAFVW 240
            YDM+A+T  + E GAL +WDL HSAGA+P++L++  AD+A+GC YKYLNGGPG+ AFV+
Sbjct: 174 RYDMEAVTRQAQEAGALIVWDLCHSAGAMPVNLNRCDADFAVGCGYKYLNGGPGAPAFVF 233

Query: 241 VNPALVDVVRQPLSGWFGHTRQFAMESTYAPSAGIARYLCGTQPITSLAMVECGLEIFAQ 300
           V    ++ VRQPL+GW GH+R F     YAP  GI R L GT P   +  +E  LE F  
Sbjct: 234 VASRHIEAVRQPLTGWHGHSRPFEFAHDYAPHPGIDRMLTGTAPQLGVIALESALEAFDG 293

Query: 301 TDMASLRSKSLALTDLFIALVEARCAAHDLKLITPREHAKRGSHVSFEHPEGYAVIQALI 360
            D+  LR KS+AL +LFI L +         L +PR+   RGS VS  H +GYA++QALI
Sbjct: 294 VDLDVLRDKSVALGNLFIELTDQELTGLGCTLASPRDAEMRGSQVSLGHAQGYAIMQALI 353

Query: 361 ARGVIGDYREPRIMRFGFTPLYTRFTEVWEAVEILGDILDNHTWNQPQFKVRNSVT 416
           AR VIGD+R P I+RFGF PLY R+ ++W+ +  L DI+    WN  +FK R SVT
Sbjct: 354 ARNVIGDFRAPDILRFGFAPLYVRYVDIWDTIAQLKDIIATDAWNTDEFKARKSVT 409


Lambda     K      H
   0.321    0.135    0.409 

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: 516
Number of extensions: 20
Number of successful extensions: 3
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: 416
Length of database: 409
Length adjustment: 31
Effective length of query: 385
Effective length of database: 378
Effective search space:   145530
Effective search space used:   145530
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 BPHYT_RS07275 BPHYT_RS07275 (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.18919.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
    7.5e-98  313.9   0.0      1e-97  313.5   0.0    1.2  1  lcl|FitnessBrowser__BFirm:BPHYT_RS07275  BPHYT_RS07275 kynureninase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS07275  BPHYT_RS07275 kynureninase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  313.5   0.0     1e-97     1e-97       1     399 [.       7     392 ..       7     393 .. 0.93

  Alignments for each domain:
  == domain 1  score: 313.5 bits;  conditional E-value: 1e-97
                                TIGR01814   1 aealdaadelkalRdeFalpkakdeneviyld.NSLalmpkaakealkeel.dkWakllveshevgkapW 68 
                                              ++aldaad+l++ R +F lp      ++iyld NSL++mp+++ + ++++l  +Wa+ l++s++  +a W
  lcl|FitnessBrowser__BFirm:BPHYT_RS07275   7 CAALDAADTLAHCRARFDLP-----ADTIYLDgNSLGAMPANVPARIEQALkHEWAHGLIRSWN--DAGW 69 
                                              579*****************.....9999*966**********99998887368**********..99** PP

                                TIGR01814  69 leldealeklla..lvakekevvvmnsltvNlhkllasfykptekRakIlleakaFPsDlyaiesqlklk 136
                                              +  +++  +  a  ++a ++ev v++s++vNl+k+l+++ +  + R +Il+e ++FP+D+y++ s  ++ 
  lcl|FitnessBrowser__BFirm:BPHYT_RS07275  70 YPAPQRTGNKIArlIGAGQDEVIVADSTSVNLFKVLVAATRMRPGRNVILAERTNFPTDVYIASSVAEMT 139
                                              ***9998766666899************************************************999998 PP

                                TIGR01814 137 leveeslvqvepreeetlrledildviekeqdeiAlvllsgvqYkt.qlfdlaaitkaarkkgalvvfDL 205
                                                    l++v+p+e           ++ + +d +A+v l++v+Ykt + +d++a+t++a++ gal+v+DL
  lcl|FitnessBrowser__BFirm:BPHYT_RS07275 140 ---GCDLRCVDPDE-----------IVSAIDDTVAIVSLTHVNYKTgKRYDMEAVTRQAQEAGALIVWDL 195
                                              ...44555666555...........88889999************************************* PP

                                TIGR01814 206 aHava.vpleLhdwdvDfAvwCsYKylnasp.a.agafvhekkakeelprlalwwwhekskrfkmeekle 272
                                              +H+++ +p++L+  d+DfAv C YKyln +p a a +fv  +++++ ++ l++w++h ++++f+ ++  +
  lcl|FitnessBrowser__BFirm:BPHYT_RS07275 196 CHSAGaMPVNLNRCDADFAVGCGYKYLNGGPgApAFVFVASRHIEAVRQPLTGWHGHSRPFEFAHDYAPH 265
                                              ****99*************************666777888888888888889999999999999999777 PP

                                TIGR01814 273 lrpaafrlsnppvlsvaalka.LelfdqaslealRkkSllLTdyleeLvkarlayklvleiitPedtaer 341
                                              +    +   + p l v al++ Le fd ++l+ lR kS++L ++++eL +++l+  l  ++++P+d + r
  lcl|FitnessBrowser__BFirm:BPHYT_RS07275 266 PGIDRMLTGTAPQLGVIALESaLEAFDGVDLDVLRDKSVALGNLFIELTDQELTG-LGCTLASPRDAEMR 334
                                              77788999999******************************************97.89************ PP

                                TIGR01814 342 .sqlslkfskedkavlkalkkrdvviDkRePnviRlaPvpLYntfkDvykavevleeil 399
                                               sq+sl ++ + +a+++al++r+v+ D+R+P+++R+  +pLY++++D+++ +  l++i+
  lcl|FitnessBrowser__BFirm:BPHYT_RS07275 335 gSQVSLGHA-QGYAIMQALIARNVIGDFRAPDILRFGFAPLYVRYVDIWDTIAQLKDII 392
                                              *********.**********************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 nodes)
Target sequences:                          1  (409 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: 7.35
//
[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)
Rules (tab-delimited)
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