Alignments for a candidate for kyn in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for kyn in Paraburkholderia bryophila 376MFSha3.1

Align Kynureninase (EC 3.7.1.3) (characterized)
to candidate H281DRAFT_04143 H281DRAFT_04143 Kynureninase

Query= reanno::BFirm:BPHYT_RS16030
         (416 letters)



>FitnessBrowser__Burk376:H281DRAFT_04143
          Length = 416

 Score =  810 bits (2092), Expect = 0.0
 Identities = 393/416 (94%), Positives = 407/416 (97%)

Query: 1   MNHRDEALALDSADPLATLRDQFALSSTTIYLDGNSLGVPPAAAAQRAQTVIGAEWGEGL 60
           M HR+EALALDSADPLATLRDQFALS+TTIYLDGNSLGVPPAAAAQRAQTVI AEWGEGL
Sbjct: 1   MKHREEALALDSADPLATLRDQFALSATTIYLDGNSLGVPPAAAAQRAQTVIAAEWGEGL 60

Query: 61  IRSWNTAGWFELPRRLGNKLAPLIGAAENEVVVTDTISINLFKLLSAAVRVANERDPKRR 120
           IRSWN AGWF LPRRLGNKLAPLIGAAENEVVVTDTISINLFKLLSAA+R+AN RDPKRR
Sbjct: 61  IRSWNAAGWFALPRRLGNKLAPLIGAAENEVVVTDTISINLFKLLSAALRLANARDPKRR 120

Query: 121 VIVSERSNFPTDLYIAQGLIEQLDRGYELRLVDDPSELPAAIGDDTAIAMITHVNYRTGY 180
           VIVSERSNFPTDLYIAQGLIEQLDRGY+LRLVDDPSELP AIG+DTAIAMITHVNYRTGY
Sbjct: 121 VIVSERSNFPTDLYIAQGLIEQLDRGYDLRLVDDPSELPEAIGEDTAIAMITHVNYRTGY 180

Query: 181 MHDMAALTKLIHDKGALALWDLAHSAGAVPVDLNGVGADYAVGCTYKYLNGGPGSPAFVW 240
           MHDMAALT+LIHDKGALALWDLAHSAGAVPVDLNGVGADYAVGCTYKYLNGGPGSPAFVW
Sbjct: 181 MHDMAALTRLIHDKGALALWDLAHSAGAVPVDLNGVGADYAVGCTYKYLNGGPGSPAFVW 240

Query: 241 VPKRHQNEFAQPLSGWWGHRAPFKMDPAYQPDDGIGRFLCGTQPMVSMSLVECGLDVFLQ 300
           VP+RHQN+FAQPLSGWWGHRAPFKMDPAYQPDDGIGRFLCGTQPMVSM+LVECGLDVFLQ
Sbjct: 241 VPQRHQNDFAQPLSGWWGHRAPFKMDPAYQPDDGIGRFLCGTQPMVSMALVECGLDVFLQ 300

Query: 301 TDMQAVRKKSLALTDLFIELVEARCSEFPLTLVTPREHAQRGSHASFEHPHGYEVMQALI 360
           TDMQA+R+KSLALTDLFIELVE RCSEFPL LVTPR H+QRGSHASFEHPHGYEVMQALI
Sbjct: 301 TDMQAIRRKSLALTDLFIELVETRCSEFPLKLVTPRAHSQRGSHASFEHPHGYEVMQALI 360

Query: 361 ARGVIGDYREPHVLRFGFTPLYTRFVDVWDAVETLREVLVKETWRAPEFAARGAVT 416
           ARGVIGDYREPHVLRFGFTPLYTRFVDVWDAVETLREVLV+ETWRAPEFAARGAVT
Sbjct: 361 ARGVIGDYREPHVLRFGFTPLYTRFVDVWDAVETLREVLVRETWRAPEFAARGAVT 416


Lambda     K      H
   0.321    0.137    0.421 

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: 741
Number of extensions: 15
Number of successful extensions: 1
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: 416
Length adjustment: 31
Effective length of query: 385
Effective length of database: 385
Effective search space:   148225
Effective search space used:   148225
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: 50 (23.9 bits)

Align candidate H281DRAFT_04143 H281DRAFT_04143 (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.3666.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   1.1e-107  346.3   0.0   1.6e-107  345.8   0.0    1.2  1  lcl|FitnessBrowser__Burk376:H281DRAFT_04143  H281DRAFT_04143 Kynureninase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_04143  H281DRAFT_04143 Kynureninase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  345.8   0.0  1.6e-107  1.6e-107       2     399 ..       8     399 ..       7     400 .. 0.89

  Alignments for each domain:
  == domain 1  score: 345.8 bits;  conditional E-value: 1.6e-107
                                    TIGR01814   2 ealdaadelkalRdeFalpkakdeneviyld.NSLalmpkaa.kealkeeldkWakllveshevgk 65 
                                                   ald ad+l++lRd+Fal        +iyld NSL++ p+aa ++a+  ++ +W++ l++s++   
  lcl|FitnessBrowser__Burk376:H281DRAFT_04143   8 LALDSADPLATLRDQFALS-----ATTIYLDgNSLGVPPAAAaQRAQTVIAAEWGEGLIRSWN--A 66 
                                                  689****************.....89999966******98751677888999***********..9 PP

                                    TIGR01814  66 apWleldealeklla..lvakekevvvmnsltvNlhkllasfykp....tekRakIlleakaFPsD 125
                                                  a W+ l+++l + la  ++a e+evvv++++++Nl+kll+++++      +kR++I++e ++FP+D
  lcl|FitnessBrowser__Burk376:H281DRAFT_04143  67 AGWFALPRRLGNKLAplIGAAENEVVVTDTISINLFKLLSAALRLanarDPKRRVIVSERSNFPTD 132
                                                  99********776666999************************98666679*************** PP

                                    TIGR01814 126 lyaiesqlklkleveeslvqvepreeetlrl.edildviekeqdeiAlvllsgvqYkt.qlfdlaa 189
                                                  ly+++  ++            +      lrl +d  ++ e+ +++ A+ ++++v+Y+t  + d+aa
  lcl|FitnessBrowser__Burk376:H281DRAFT_04143 133 LYIAQGLIEQL----------DRG--YDLRLvDDPSELPEAIGEDTAIAMITHVNYRTgYMHDMAA 186
                                                  ***86544332..........322..24554055668889******************999***** PP

                                    TIGR01814 190 itkaarkkgalvvfDLaHava.vpleLhdwdvDfAvwCsYKylnaspaagafvhekkakeelprla 254
                                                  +t++ + kgal+ +DLaH+++ vp++L+  ++D+Av C+YKyln +p + afv+  ++++++++++
  lcl|FitnessBrowser__Burk376:H281DRAFT_04143 187 LTRLIHDKGALALWDLAHSAGaVPVDLNGVGADYAVGCTYKYLNGGPGSPAFVWVPQRHQNDFAQP 252
                                                  ********************99*************************8899999999999888765 PP

                                    TIGR01814 255 ..lwwwhekskrfkmeeklelrp..aafrlsnppvlsvaalka.LelfdqaslealRkkSllLTdy 315
                                                    +ww+h  +++++  +  +++     f   ++p++s+a +++ L++f q++++a+R+kSl+LTd+
  lcl|FitnessBrowser__Burk376:H281DRAFT_04143 253 lsGWWGHRAPFKMDPAY--QPDDgiGRFLCGTQPMVSMALVECgLDVFLQTDMQAIRRKSLALTDL 316
                                                  22799999886665555..6666525566669********************************** PP

                                    TIGR01814 316 leeLvkarlayklvleiitPedtaer.sqlslkfskedkavlkalkkrdvviDkRePnviRlaPvp 380
                                                  ++eLv++r+++   l+++tP+ +++r s+ s++++ + ++v++al++r+v+ D+ReP v+R+  +p
  lcl|FitnessBrowser__Burk376:H281DRAFT_04143 317 FIELVETRCSE-FPLKLVTPRAHSQRgSHASFEHP-HGYEVMQALIARGVIGDYREPHVLRFGFTP 380
                                                  **********7.89*********************.9***************************** PP

                                    TIGR01814 381 LYntfkDvykavevleeil 399
                                                  LY++f+Dv++ave+l+e+l
  lcl|FitnessBrowser__Burk376:H281DRAFT_04143 381 LYTRFVDVWDAVETLREVL 399
                                                  ****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 nodes)
Target sequences:                          1  (416 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 6.98
//
[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