Alignments for a candidate for kyn in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for kyn in Halomonas desiderata SP1

Align Kynureninase (EC 3.7.1.3) (characterized)
to candidate WP_086508298.1 BZY95_RS01815 kynureninase

Query= reanno::Cup4G11:RR42_RS15385
         (418 letters)



>NCBI__GCF_002151265.1:WP_086508298.1
          Length = 428

 Score =  385 bits (989), Expect = e-111
 Identities = 209/431 (48%), Positives = 272/431 (63%), Gaps = 21/431 (4%)

Query: 4   MTREQCLALDQEDPLRRLRDQFALPQGVIYLDGNSLGARPRSAAARAAEVVSEEWGTGLI 63
           +T +    LD++DPL   R++FALP+G IYLDGNSLGA+PR+A A A + +  +W   LI
Sbjct: 3   LTLDDVRELDRQDPLATFRNRFALPEGTIYLDGNSLGAQPRAAVA-AVDGLMSQWRDSLI 61

Query: 64  RSWNTAGWFELPQRLGNMLAPLIGAGEDEVVVTDTTSSNLFKVLAAALRVQQTRDPK--- 120
           + WN  GWF+ P+RLG+ LAPL+GA   EV+VTDT + N+FK+L      Q+  + +   
Sbjct: 62  QGWNQ-GWFDAPERLGDRLAPLLGAEPGEVLVTDTITHNIFKLLGYITEGQKGTEGQKGT 120

Query: 121 ------------RKVIVSEASNFPTDLYIAQGLADLLQQGYSLRLVNAPEEIDAAVDADT 168
                       R VI+SE  NFPTD YIAQG       G+  R+V   E +DA +D   
Sbjct: 121 EGQKGTEGQGRGRPVILSEGGNFPTDGYIAQGFCRF--GGFEHRVVPEGEALDAYLDERV 178

Query: 169 AVLMLTHVNYKTGEMLDMASVTEMAHARGALTVWDLAHSAGAVPVALKASGADYAVGCTY 228
           A ++L+HV+Y+TG + DMA++T   HA GA  VWDLAHSAGA+ V L A    YAVGCTY
Sbjct: 179 AAVVLSHVHYRTGRLRDMAAITRQVHASGAEVVWDLAHSAGALLVDLAACDVRYAVGCTY 238

Query: 229 KYLNGGPGSPAFLWVAPSLRDAFWQPLSGWWGHAAPFAMEPGYRPREGVARFLCGTQPIA 288
           KYLNGGPG+PAFL+V    +   WQPLSGW GHAAPFA E  Y P  G++RF  GT    
Sbjct: 239 KYLNGGPGAPAFLYVRRDCQAQAWQPLSGWLGHAAPFAFEADYAPAPGISRFRTGTHSPL 298

Query: 289 SLAMVECGLDIYAQTDMAVLRAKSLMLTDLFIALVETRCAAHPLELVTPRAHARRGSHVS 348
           + A +E  L ++ + D+A LR KS  L +LF   +      H +  +TP   A+RGS V 
Sbjct: 299 AFAALEASLSLWQEVDLAQLRRKSQRLIELFRESLSGCLEEHGISDITP-DEAQRGSQVG 357

Query: 349 FAHPD-GFAVVQALIERGVIGDYREPRIARFGFTPLYTSFTEVWDAVEILRDVLDSGTYK 407
               + G+A+VQALIERGVIGDYREP + RFGF PLY S  +VW A + LR+VL +G + 
Sbjct: 358 LVEREHGYAIVQALIERGVIGDYREPGLMRFGFAPLYLSHEDVWQAAQHLREVLGAGEHL 417

Query: 408 AERHQTRGLVT 418
           A R Q RG VT
Sbjct: 418 APRFQQRGAVT 428


Lambda     K      H
   0.321    0.135    0.410 

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: 567
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: 418
Length of database: 428
Length adjustment: 32
Effective length of query: 386
Effective length of database: 396
Effective search space:   152856
Effective search space used:   152856
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 WP_086508298.1 BZY95_RS01815 (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.26382.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
      3e-79  252.7   0.0    1.2e-78  250.7   0.0    1.9  1  lcl|NCBI__GCF_002151265.1:WP_086508298.1  BZY95_RS01815 kynureninase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086508298.1  BZY95_RS01815 kynureninase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  250.7   0.0   1.2e-78   1.2e-78       2     399 ..       9     411 ..       8     412 .. 0.91

  Alignments for each domain:
  == domain 1  score: 250.7 bits;  conditional E-value: 1.2e-78
                                 TIGR01814   2 ealdaadelkalRdeFalpkakdeneviyld.NSLalmpkaakealkeeldkWakllveshevgkapWl 69 
                                               ++ld +d+l+++R++Falp     + +iyld NSL+++p+aa +a++  + +W + l+++++   + W+
  lcl|NCBI__GCF_002151265.1:WP_086508298.1   9 RELDRQDPLATFRNRFALP-----EGTIYLDgNSLGAQPRAAVAAVDGLMSQWRDSLIQGWN---QGWF 69 
                                               689****************.....88999966******************************...78** PP

                                 TIGR01814  70 eldealeklla..lvakekevvvmnsltvNlhkllasfykp...................tekRakIll 117
                                               + +e+l + la  l+a+  ev v++++t N++kll  + +                       R +Il+
  lcl|NCBI__GCF_002151265.1:WP_086508298.1  70 DAPERLGDRLAplLGAEPGEVLVTDTITHNIFKLLGYITEGqkgtegqkgtegqkgtegqGRGRPVILS 138
                                               ******9988889**********************87766566899999*99999977766789***** PP

                                 TIGR01814 118 eakaFPsDlyaiesqlklkleveeslvqvepreeetlrledildviekeqdeiAlvllsgvqYkt.qlf 185
                                               e  +FP+D y+++  ++     e+    v p+        ++ld  +  ++++A v+ls+v+Y+t +l+
  lcl|NCBI__GCF_002151265.1:WP_086508298.1 139 EGGNFPTDGYIAQGFCRFG-GFEH---RVVPEG-------EALD--AYLDERVAAVVLSHVHYRTgRLR 194
                                               *****************99.2222...122222.......3333..445679***************** PP

                                 TIGR01814 186 dlaaitkaarkkgalvvfDLaHava.vpleLhdwdvDfAvwCsYKylnaspaagafvhekkakeelprl 253
                                               d+aait++ ++ ga vv+DLaH+++ + ++L + dv +Av C+YKyln +p a af++ +   + ++++
  lcl|NCBI__GCF_002151265.1:WP_086508298.1 195 DMAAITRQVHASGAEVVWDLAHSAGaLLVDLAACDVRYAVGCTYKYLNGGPGAPAFLYVRRDCQAQAWQ 263
                                               ************************99*************************888888888888888886 PP

                                 TIGR01814 254 a..lwwwhekskrfkmeeklelrpaafrlsnppvlsvaalka.LelfdqaslealRkkSllLTdyleeL 319
                                               +  +w +h+ +++f+ ++  ++  + fr  + + l+ aal+a L l+++++l++lR+kS  L +++ e 
  lcl|NCBI__GCF_002151265.1:WP_086508298.1 264 PlsGWLGHAAPFAFEADYAPAPGISRFRTGTHSPLAFAALEAsLSLWQEVDLAQLRRKSQRLIELFRES 332
                                               5227999***********888888********************************************* PP

                                 TIGR01814 320 vkarlayklvleiitPedtaer.sqlslkfskedkavlkalkkrdvviDkRePnviRlaPvpLYntfkD 387
                                               +   l++   ++ itP +  +r sq+ l   ++ +a+++al++r+v+ D+ReP  +R+  +pLY +++D
  lcl|NCBI__GCF_002151265.1:WP_086508298.1 333 LSGCLEE-HGISDITPDEA-QRgSQVGLVEREHGYAIVQALIERGVIGDYREPGLMRFGFAPLYLSHED 399
                                               *999997.6889999*998.666********9************************************* PP

                                 TIGR01814 388 vykavevleeil 399
                                               v++a ++l+e+l
  lcl|NCBI__GCF_002151265.1:WP_086508298.1 400 VWQAAQHLREVL 411
                                               *********997 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: 0.06u 0.01s 00:00:00.06 Elapsed: 00:00:00.06
# Mc/sec: 2.57
//
[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 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