Alignments for a candidate for kyn in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for kyn in Dinoroseobacter shibae DFL-12

Align Kynureninase (EC 3.7.1.3) (characterized)
to candidate 3607822 Dshi_1230 kynureninase (RefSeq)

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



>FitnessBrowser__Dino:3607822
          Length = 393

 Score =  385 bits (989), Expect = e-111
 Identities = 193/397 (48%), Positives = 265/397 (66%), Gaps = 7/397 (1%)

Query: 20  RSQFALPEGVIYLDGNSLGARPVAALARAQAVIAEEWGNGLIRSWNNAGWADLSLRLGNR 79
           R  F LPEGVIYLDGNSLG  P  A A     +  EWG  LIR WN AGW D   RLG+R
Sbjct: 4   RDAFDLPEGVIYLDGNSLGPLPRRAEAAVARAMQAEWGAMLIRGWNEAGWMDQPDRLGDR 63

Query: 80  LAPLIGARDNEVAITDTTSINLFKVLSAALTVQRQRQPGRKVIVSEASNFPTDLYIAEGL 139
           +APLIGA    V + +T SI +F+ L+AAL+++    PGRKVI++EA NFP+DLY+A+GL
Sbjct: 64  IAPLIGAAPGTVTVGETLSIRVFQGLAAALSLR----PGRKVILTEAGNFPSDLYMAQGL 119

Query: 140 AELLQQGYSLRLVNSPDELPQAIDQDVAVVMLTHVNYKTGYMYDMQALTALSHECGALSI 199
            + L QG+ LR + +  E+P A+  +VAV+MLT V+Y++G  +DM ALTA +H  GAL++
Sbjct: 120 IDALGQGHVLRALPAT-EIPAALTDEVAVLMLTEVDYRSGARHDMAALTAQAHGVGALTL 178

Query: 200 WDLAHSAGAVPIDLHQAGADYAIGCTYKYLNGGPGSQAFVWVNPALVDVVRQPLSGWFGH 259
           WDLAHSAGA+P+ L +  AD+A GCTYKYLNGGPG+ AF +  P   ++ R  L+GW GH
Sbjct: 179 WDLAHSAGALPVALTRCNADFAAGCTYKYLNGGPGAPAFFYARPDHSEITRPILAGWLGH 238

Query: 260 TRQFAMESTYAPSAGIARYLCGTQPITSLAMVECGLEIFAQTDMASLRSKSLALTDLFIA 319
              F     YAP  G AR+  GT P+  +A ++  L+IF   D+A+L ++++ L D    
Sbjct: 239 AAPFDFAPDYAPGPGRARFRIGTPPVLQMAALDAALDIFDGVDIAALHARAIVLADRLAT 298

Query: 320 LVEARCAAHDLKLITPREHAKRGSHVSFEHPEGYAVIQALIARGVIGDYREPRIMRFGFT 379
             EA C   DL+ +TP + A+RGS ++F HP GYA++QALIA+GVIGD+R P I+RFG T
Sbjct: 299 GFEAVCP--DLRRLTPMDPARRGSQIAFAHPNGYAMVQALIAQGVIGDFRAPDILRFGLT 356

Query: 380 PLYTRFTEVWEAVEILGDILDNHTWNQPQFKVRNSVT 416
           PLY    ++  A+E    +++   W+ P ++ RN VT
Sbjct: 357 PLYLDAGDIDTAIERFAQVIEGRLWDDPAYRTRNKVT 393


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: 509
Number of extensions: 19
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: 393
Length adjustment: 31
Effective length of query: 385
Effective length of database: 362
Effective search space:   139370
Effective search space used:   139370
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 3607822 Dshi_1230 (kynureninase (RefSeq))
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.12881.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    1.7e-80  256.8   0.0      3e-80  256.0   0.0    1.3  1  lcl|FitnessBrowser__Dino:3607822  Dshi_1230 kynureninase (RefSeq)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3607822  Dshi_1230 kynureninase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  256.0   0.0     3e-80     3e-80      14     399 ..       4     376 ..       2     377 .. 0.93

  Alignments for each domain:
  == domain 1  score: 256.0 bits;  conditional E-value: 3e-80
                         TIGR01814  14 RdeFalpkakdeneviyld.NSLalmpkaakealkeeld.kWakllveshevgkapWleldealeklla..lvakek 86 
                                       Rd+F lp     + viyld NSL+  p++a++a+  +++ +W+++l+++++  +a W++ + +l +  a  ++a   
  lcl|FitnessBrowser__Dino:3607822   4 RDAFDLP-----EGVIYLDgNSLGPLPRRAEAAVARAMQaEWGAMLIRGWN--EAGWMDQPDRLGDRIAplIGAAPG 73 
                                       9******.....99****66**********99998777648**********..***********99888899999** PP

                         TIGR01814  87 evvvmnsltvNlhkllasfykptekRakIlleakaFPsDlyaiesqlklkleveeslvqvepreeetlrledildvi 163
                                        v+v ++l++ +++ la+++   + R++Il+ea +FPsDly+++  +                + + lr   ++++ 
  lcl|FitnessBrowser__Dino:3607822  74 TVTVGETLSIRVFQGLAAALSLRPGRKVILTEAGNFPSDLYMAQGLIDAL------------GQGHVLRALPATEIP 138
                                       ******************************************87655444............223467777888888 PP

                         TIGR01814 164 ekeqdeiAlvllsgvqYkt.qlfdlaaitkaarkkgalvvfDLaHava.vpleLhdwdvDfAvwCsYKylnaspaag 238
                                       ++ +de+A+ +l++v Y++    d+aa+t++a+  gal  +DLaH+++ +p+ L   ++DfA  C+YKyln +p a 
  lcl|FitnessBrowser__Dino:3607822 139 AALTDEVAVLMLTEVDYRSgARHDMAALTAQAHGVGALTLWDLAHSAGaLPVALTRCNADFAAGCTYKYLNGGPGAP 215
                                       8999***************8899************************99*************************888 PP

                         TIGR01814 239 afvhekkakee..lprlalwwwhekskrfkmeeklelrpaafrlsnppvlsvaalka.LelfdqaslealRkkSllL 312
                                       af ++++ ++e  +p la+w +h+ ++ f+ ++   + +a fr+ +ppvl++aal a L++fd ++++al ++ ++L
  lcl|FitnessBrowser__Dino:3607822 216 AFFYARPDHSEitRPILAGWLGHAAPFDFAPDYAPGPGRARFRIGTPPVLQMAALDAaLDIFDGVDIAALHARAIVL 292
                                       99998887776337889****************999999************************************** PP

                         TIGR01814 313 TdyleeLvkarlayklvleiitPedtaer.sqlslkfskedkavlkalkkrdvviDkRePnviRlaPvpLYntfkDv 388
                                        d l    +a +     l+ +tP d a+r sq+ ++++ + +a+++al++++v+ D+R+P+++R+  +pLY    D+
  lcl|FitnessBrowser__Dino:3607822 293 ADRLATGFEAVCPD---LRRLTPMDPARRgSQIAFAHP-NGYAMVQALIAQGVIGDFRAPDILRFGLTPLYLDAGDI 365
                                       *************7...9********************.9************************************* PP

                         TIGR01814 389 ykavevleeil 399
                                        +a+e + +++
  lcl|FitnessBrowser__Dino:3607822 366 DTAIERFAQVI 376
                                       *****998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (400 nodes)
Target sequences:                          1  (393 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: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.05
# Mc/sec: 3.12
//
[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