GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bkdB in Pseudomonas stutzeri RCH2

Align 2-keto-isovalerate dehydrogenase component β subunit (EC 1.2.4.4) (characterized)
to candidate GFF1390 Psest_1427 Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, beta subunit

Query= metacyc::MONOMER-11684
         (327 letters)



>lcl|FitnessBrowser__psRCH2:GFF1390 Psest_1427
           Pyruvate/2-oxoglutarate dehydrogenase complex,
           dehydrogenase (E1) component, eukaryotic type, beta
           subunit
          Length = 340

 Score =  265 bits (676), Expect = 2e-75
 Identities = 139/316 (43%), Positives = 204/316 (64%), Gaps = 9/316 (2%)

Query: 13  AMKEEMERDSRVFVLGEDVGRKGGVFKATAGLYEQFGEERVMDTPLAESAIAGVGIGAAM 72
           A+ +EM  D +VFV+GED+G+ GGVF  T GLYE+FG+ R+ DTP++E+A  G  +GAA 
Sbjct: 19  AVAQEMRLDPKVFVMGEDIGQLGGVFGNTRGLYEEFGKTRIRDTPISETAFIGAAVGAAS 78

Query: 73  YGMRPIAEMQFADFIMPAVNQIISEAAKIRYRSNNDWSCPIVVRAPYGGGVHGALYHSQS 132
            GMRPI E+ F DF    ++ I +  AK  Y S      P+V+ A  G G   A  HSQ 
Sbjct: 79  DGMRPIVELMFVDFFGVCMDAIYNLMAKNTYFSGGKVPVPMVLMASTGAGYSDAGQHSQC 138

Query: 133 VEAIFANQPGLKIVMPSTPYDAKGLLKAAVRDEDPVLFFEHKRAYRL-----IKG---EV 184
           +   FA+ PG+K+V+PS  YDAKGL+ AA+RD++PV++  HK    +      KG    V
Sbjct: 139 LYGTFAHLPGMKVVVPSNAYDAKGLMTAAIRDDNPVVYLFHKALQGMGWLGTEKGATVPV 198

Query: 185 PADDYVLPIGKADVKREGDDITVITYGLCVHFALQAAERLEKDGISAHVVDLRTVYPLDK 244
           P + Y++ IGKA   REG D+++++ G  VH AL+AA +LEKDG+SA V+DLR++ PLD+
Sbjct: 199 PEEPYIVEIGKAKTVREGRDVSLVSLGAGVHHALRAAAQLEKDGVSAEVIDLRSLVPLDR 258

Query: 245 EAIIEAASKTGKVLLVTEDTKEGSIMSEVAAIISEHCLFDLDAPIKRLAGPDIPAMPYAP 304
           E +I +  KTG+++++ ED     +  E+ A + EH +  L A  +R+A PDIP +P+ P
Sbjct: 259 EHVIASVRKTGRLIVIDEDYHSFGVSGEIIASVVEHDIGMLKARPQRVAFPDIP-IPFTP 317

Query: 305 TMEKYFMVNPDKVEAA 320
            ME++ + N DK+ AA
Sbjct: 318 VMEQWALPNADKIVAA 333


Lambda     K      H
   0.319    0.136    0.392 

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: 297
Number of extensions: 16
Number of successful extensions: 3
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: 327
Length of database: 340
Length adjustment: 28
Effective length of query: 299
Effective length of database: 312
Effective search space:    93288
Effective search space used:    93288
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: 49 (23.5 bits)

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:

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:

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:

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 preprint on GapMind for carbon sources, or view the source code.

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