Alignments for a candidate for kyn in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for kyn in Acidovorax sp. GW101-3H11

Align Kynureninase (EC 3.7.1.3) (characterized)
to candidate Ac3H11_1157 Kynureninase (EC 3.7.1.3)

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_1157
          Length = 436

 Score =  513 bits (1321), Expect = e-150
 Identities = 265/435 (60%), Positives = 315/435 (72%), Gaps = 26/435 (5%)

Query: 5   TREQCLALDQEDPLRRLRDQFALPQGVIYLDGNSLGARPRSAAARAAEVVSEEWGTGLIR 64
           T + C ALD +DPL  L   FALP GVIYLDGNSLG  P++AAAR A+VV+ EW T LI+
Sbjct: 4   TLQDCRALDAQDPLAPLHSHFALPPGVIYLDGNSLGVAPKAAAARVADVVTREWATDLIK 63

Query: 65  SWNTAGWFELPQRLGNMLAPLIGAGEDEVVVTDTTSSNLFKVLAAALRVQQTRDPKRKVI 124
           SWNTA WF+LPQRLGN LAPLIGAG +EVV TD+TS NL+KVL+AAL + +   P RK I
Sbjct: 64  SWNTASWFDLPQRLGNQLAPLIGAGPNEVVCTDSTSINLYKVLSAALNIAREDSPARKRI 123

Query: 125 VSEASNFPTDLYIAQGLADLLQQGYSLRLVNAPEEIDAAVDADTAVLMLTHVNYKTGEML 184
           VSE SNFPTDLYIA+GL    ++G  L LV  PEEI+AA+ +D AVLMLTHVNY+TG M 
Sbjct: 124 VSERSNFPTDLYIAEGLCK--ERGLELVLVE-PEEINAALTSDVAVLMLTHVNYRTGAMH 180

Query: 185 DMASVTEMAHARGALTVWDLAHSAGAVPVALKASGADYAVGCTYKYLNGGPGSPAFLWVA 244
           DMA++T  AHA+G L VWDLAHSAGAVPV L  +GAD+++GC YKYLNGGPG+PAF+WV 
Sbjct: 181 DMAAITAAAHAQGILCVWDLAHSAGAVPVDLNGAGADFSIGCGYKYLNGGPGAPAFVWVH 240

Query: 245 PSLRDAFWQPLSGWWGHAAPFAMEPGYRPREGVARFLCGTQPIASLAMVECGLDIYAQTD 304
                 FWQPLSGWWGHAAPFA  P Y+P  G+ R+LCGTQPI SL+ ++CGLD++    
Sbjct: 241 SRHASRFWQPLSGWWGHAAPFAFTPDYQPAPGITRYLCGTQPIISLSALQCGLDVFTAAQ 300

Query: 305 ----MAVLRAKSLMLTDLFIALVETRCAAHPLELVTPRAHARRGSHVSFAHPDG------ 354
               MA LRAKSL LTDLFI LVE RCA H L L TPR HA+RGS V     +G      
Sbjct: 301 SLGGMAALRAKSLALTDLFIQLVEERCAGHGLGLATPREHAQRGSQVCLTRDEGAGVGGQ 360

Query: 355 ----FAVVQALIERGVIGDYRE--------PRIARFGFTPLYTSFTEVWDAVEILRDVLD 402
               +A+VQALI RGVIGD+R+          I RFGFTPLY  F +VW+AVE LR VL+
Sbjct: 361 GSGAYAIVQALIARGVIGDFRKGDGGTGRHKDILRFGFTPLYLGFEDVWNAVEHLRQVLE 420

Query: 403 SGTY-KAERHQTRGL 416
           SG + KAE +QT  +
Sbjct: 421 SGEWQKAEFNQTHAV 435


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: 635
Number of extensions: 39
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 418
Length of database: 436
Length adjustment: 32
Effective length of query: 386
Effective length of database: 404
Effective search space:   155944
Effective search space used:   155944
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: 51 (24.3 bits)

Align candidate Ac3H11_1157 (Kynureninase (EC 3.7.1.3))
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.28256.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
    6.1e-99  317.5   0.0    7.6e-99  317.2   0.0    1.1  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1157  Kynureninase (EC 3.7.1.3)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1157  Kynureninase (EC 3.7.1.3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  317.2   0.0   7.6e-99   7.6e-99       1     400 []       8     420 ..       8     420 .. 0.91

  Alignments for each domain:
  == domain 1  score: 317.2 bits;  conditional E-value: 7.6e-99
                                        TIGR01814   1 aealdaadelkalRdeFalpkakdeneviyld.NSLalmpkaakeal.keeldkWakllves 60 
                                                      ++alda+d+l+ l ++Falp       viyld NSL+++pkaa++ + + ++ +Wa  l++s
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1157   8 CRALDAQDPLAPLHSHFALP-----PGVIYLDgNSLGVAPKAAAARVaDVVTREWATDLIKS 64 
                                                      579*****************.....89****66*******98876551566789******** PP

                                        TIGR01814  61 hevgkapWleldealeklla..lvakekevvvmnsltvNlhkllasfykp....tekRakIl 116
                                                      ++  +a+W++l+++l + la  ++a  +evv ++s+++Nl+k+l+++++     ++ R+ I+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1157  65 WN--TASWFDLPQRLGNQLAplIGAGPNEVVCTDSTSINLYKVLSAALNIaredSPARKRIV 124
                                                      **..9**********877777999************************987778999***** PP

                                        TIGR01814 117 leakaFPsDlyaiesqlklkleveeslvqvepreeetlrledildviekeqdeiAlvllsgv 178
                                                      +e ++FP+Dly++e  +k +      lv vep+e           + ++ + ++A+ +l++v
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1157 125 SERSNFPTDLYIAEGLCKER---GLELVLVEPEE-----------INAALTSDVAVLMLTHV 172
                                                      ***************99998...77799999999...........33445678********* PP

                                        TIGR01814 179 qYkt.qlfdlaaitkaarkkgalvvfDLaHava.vpleLhdwdvDfAvwCsYKylnaspaag 238
                                                      +Y+t  + d+aait+aa+++g l v+DLaH+++ vp++L+ +++Df + C YKyln +p a 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1157 173 NYRTgAMHDMAAITAAAHAQGILCVWDLAHSAGaVPVDLNGAGADFSIGCGYKYLNGGPGAP 234
                                                      ****99**************************99*************************889 PP

                                        TIGR01814 239 afvhekkakeelprla..lwwwhekskrfkmeeklelrpaafrlsnppvlsvaalka.Lelf 297
                                                      afv+ + +++++++++  +ww+h+ +++f+ +++ ++  + +   ++p++s+ al++ L++f
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1157 235 AFVWVHSRHASRFWQPlsGWWGHAAPFAFTPDYQPAPGITRYLCGTQPIISLSALQCgLDVF 296
                                                      9999999999999975337**************98888899********************* PP

                                        TIGR01814 298 dqas....lealRkkSllLTdyleeLvkarlayklvleiitPedtaer.sqlslkfs..... 349
                                                        a+    ++alR+kSl+LTd++++Lv+ r+a    l ++tP+++a+r sq+ l+ +     
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1157 297 TAAQslggMAALRAKSLALTDLFIQLVEERCAG-HGLGLATPREHAQRgSQVCLTRDegagv 357
                                                      99855555************************8.79********************999999 PP

                                        TIGR01814 350 ....kedkavlkalkkrdvviDkReP........nviRlaPvpLYntfkDvykavevleeil 399
                                                          + ++a+++al++r+v+ D+R+         +++R+  +pLY  f+Dv++ave+l+++l
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1157 358 ggqgSGAYAIVQALIARGVIGDFRKGdggtgrhkDILRFGFTPLYLGFEDVWNAVEHLRQVL 419
                                                      9999999****************9752222222279***********************998 PP

                                        TIGR01814 400 e 400
                                                      e
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1157 420 E 420
                                                      6 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 nodes)
Target sequences:                          1  (436 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: 8.05
//
[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