Alignments for a candidate for kyn in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for kyn in Phaeobacter inhibens BS107

Align Kynureninase (EC 3.7.1.3) (characterized)
to candidate GFF981 PGA1_c09980 kynureninase KynU

Query= reanno::pseudo13_GW456_L13:PfGW456L13_4288
         (416 letters)



>FitnessBrowser__Phaeo:GFF981
          Length = 397

 Score =  395 bits (1015), Expect = e-114
 Identities = 193/397 (48%), Positives = 265/397 (66%), Gaps = 7/397 (1%)

Query: 20  RQQFALPEGVIYLDGNSLGARPVAALARAQAVIAEEWGNGLIRSWNSAGWRDLPERLGNR 79
           +  F+LPEG+IYLDGNSLG  P A   R +  I +EWG  LI  WN AGW   P  +G+R
Sbjct: 8   KAMFSLPEGMIYLDGNSLGPMPRATAERVRGTIEDEWGEMLITGWNKAGWMQKPTAIGDR 67

Query: 80  LGGLIGAGDGEVVVTDTTSINLFKVLSAALRVQATRAPTRRVIVTETGNFPTDLYIAEGL 139
           +  LIGA  G VV+ DT SI +++ +++AL +     PTR+V++++ GNFP+DLY+ EGL
Sbjct: 68  IARLIGAEPGHVVMGDTLSIKVYQAVASALELN----PTRKVVLSDNGNFPSDLYMVEGL 123

Query: 140 ADMLQQGYTLRLVDSPQELPQAIDQDTAVVMLTHVNYKTGYMHDMQALTTLTHECGALAI 199
              L   Y+LR+V +P+E+   +  D AV+MLT V+Y+TG  HDM+ALT   H  G + +
Sbjct: 124 VKSLGPDYSLRVV-APEEVSANLTDDIAVLMLTEVDYRTGRKHDMKALTEQAHAAGVVTV 182

Query: 200 WDLAHSAGAVPVDLHQARADYAIGCTYKYLNGGPGSQAFVWVSPELCDLVAQPLSGWFGH 259
           WDLAHSAGA+PVDL   +AD+A+GCTYKYLN GPG  AF++V+P   +     LSGW GH
Sbjct: 183 WDLAHSAGALPVDLAGCKADFAVGCTYKYLNSGPGGPAFIYVAPRHAEKARPALSGWLGH 242

Query: 260 SRQFAMESHYQPSSGIARYLCGTQPITSLAMVECGLDVFAQTDMASLRSKSLALTDLFIQ 319
           +  F  + +Y+P +GI R   GT P+  LA +E  +D++   DMA +R+KS+ L DLFI 
Sbjct: 243 AAPFDFDLNYKPGNGIERMRVGTPPVLQLAALEASMDIWDMADMADVRAKSIELCDLFIT 302

Query: 320 LVEQRCAAHELTLVTPREHAKRGSHVSFEHPQGYAVIQALIARGVIGDYREPRIMRFGFT 379
            VE RC   +LTL +PR+   RGS VSF   +GYA +QALIARGV+GD+R P IMRFGFT
Sbjct: 303 EVESRCP--DLTLASPRDGTVRGSQVSFRFHEGYAAMQALIARGVVGDFRSPDIMRFGFT 360

Query: 380 PLYTSFTEVWDAVQILGDILDQKTWSQEQFQIRHSVT 416
           PLY    +V  AV I+ D++    W   +++ R++VT
Sbjct: 361 PLYIDQGDVRAAVDIIEDVITNALWDSAEYKTRNAVT 397


Lambda     K      H
   0.321    0.135    0.412 

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: 479
Number of extensions: 18
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: 416
Length of database: 397
Length adjustment: 31
Effective length of query: 385
Effective length of database: 366
Effective search space:   140910
Effective search space used:   140910
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 GFF981 PGA1_c09980 (kynureninase KynU)
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.23129.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    7.3e-92  294.2   0.0    9.7e-92  293.8   0.0    1.1  1  lcl|FitnessBrowser__Phaeo:GFF981  PGA1_c09980 kynureninase KynU


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF981  PGA1_c09980 kynureninase KynU
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  293.8   0.0   9.7e-92   9.7e-92      16     399 ..      10     380 ..       3     381 .. 0.93

  Alignments for each domain:
  == domain 1  score: 293.8 bits;  conditional E-value: 9.7e-92
                         TIGR01814  16 eFalpkakdeneviyld.NSLalmpkaakealk.eeldkWakllveshevgkapWleldealeklla..lvakekev 88 
                                        F lp     + +iyld NSL+ mp+a++e ++  + d+W+++l+++++  ka W++ ++a+ +  a  ++a+   v
  lcl|FitnessBrowser__Phaeo:GFF981  10 MFSLP-----EGMIYLDgNSLGPMPRATAERVRgTIEDEWGEMLITGWN--KAGWMQKPTAIGDRIArlIGAEPGHV 79 
                                       67777.....77899966*******9988777615669***********..***********99888889999999* PP

                         TIGR01814  89 vvmnsltvNlhkllasfykptekRakIlleakaFPsDlyaiesqlklkleveeslvqvepreeetlrledildviek 165
                                       v+ ++l++ +++ +as+++  ++R+++l+++ +FPsDly++e  +k    ++ sl+ v p+e           v ++
  lcl|FitnessBrowser__Phaeo:GFF981  80 VMGDTLSIKVYQAVASALELNPTRKVVLSDNGNFPSDLYMVEGLVKSL-GPDYSLRVVAPEE-----------VSAN 144
                                       ******************************************987765.6777777777777...........7788 PP

                         TIGR01814 166 eqdeiAlvllsgvqYkt.qlfdlaaitkaarkkgalvvfDLaHava.vpleLhdwdvDfAvwCsYKylnasp.a.ag 238
                                        +d+iA+ +l++v Y+t +  d++a+t++a++ g + v+DLaH+++ +p++L   ++DfAv C+YKyln++p   a 
  lcl|FitnessBrowser__Phaeo:GFF981 145 LTDDIAVLMLTEVDYRTgRKHDMKALTEQAHAAGVVTVWDLAHSAGaLPVDLAGCKADFAVGCTYKYLNSGPgGpAF 221
                                       89*******************************************99*************************54556 PP

                         TIGR01814 239 afvhekkakeelprlalwwwhekskrfkmeeklelrpaafrlsnppvlsvaalka.LelfdqaslealRkkSllLTd 314
                                       ++v +++a++ +p+l++w +h+ ++ f+ ++k     + +r+ +ppvl++aal+a ++++d a+++++R+kS+ L d
  lcl|FitnessBrowser__Phaeo:GFF981 222 IYVAPRHAEKARPALSGWLGHAAPFDFDLNYKPGNGIERMRVGTPPVLQLAALEAsMDIWDMADMADVRAKSIELCD 298
                                       66778889999999*****************8888889*************************************** PP

                         TIGR01814 315 yleeLvkarlayklvleiitPedtaer.sqlslkfskedkavlkalkkrdvviDkRePnviRlaPvpLYntfkDvyk 390
                                       +++  v+ r+     l++++P+d + r sq+s++f  e +a ++al++r+vv D+R+P+++R+  +pLY    Dv+ 
  lcl|FitnessBrowser__Phaeo:GFF981 299 LFITEVESRCPD---LTLASPRDGTVRgSQVSFRFH-EGYAAMQALIARGVVGDFRSPDIMRFGFTPLYIDQGDVRA 371
                                       ***********8...*********************.**************************************** PP

                         TIGR01814 391 avevleeil 399
                                       av+++e+++
  lcl|FitnessBrowser__Phaeo:GFF981 372 AVDIIEDVI 380
                                       ******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 nodes)
Target sequences:                          1  (397 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.30
//
[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