GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdB in Marinobacter adhaerens HP15

Align 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) (EC 1.2.4.4) (characterized)
to candidate GFF63 HP15_63 2-oxoisovalerate dehydrogenase, E1 component, beta subunit

Query= reanno::Smeli:SMc03202
         (337 letters)



>FitnessBrowser__Marino:GFF63
          Length = 268

 Score =  407 bits (1046), Expect = e-118
 Identities = 183/266 (68%), Positives = 220/266 (82%)

Query: 70  MAAYGLKPCVEIQFADYMYPAYDQLTQEAARIRYRSNGDFTCPIVVRMPTGGGIFGGQTH 129
           M AYGL+P  EIQFADY+ PAYDQL  EAAR+RYRS G+F  PI VR P GGGIFGGQTH
Sbjct: 1   MGAYGLRPVAEIQFADYILPAYDQLVSEAARLRYRSGGEFWAPITVRSPYGGGIFGGQTH 60

Query: 130 SQSPEALFTHVCGLKVVVPSNPYDAKGLLISAIEDPDPVMFLEPKRLYNGPFDGHHERPV 189
           SQSPEA+F H+ GLK V+PSNPYDAKGLLIS+IE  DP++FLEPKR+YNGPFDGHHER +
Sbjct: 61  SQSPEAIFAHITGLKTVIPSNPYDAKGLLISSIESDDPIIFLEPKRIYNGPFDGHHERQI 120

Query: 190 TAWSKHELGDVPDGHYTIPIGKAEIRRKGSGVTVIAYGTMVHVALAAAEETGIDAEVIDL 249
            +W+ H    VP+GHYT+P+GKA   R GS VTV+AYG MVHVA A  EE+G+DAE++DL
Sbjct: 121 KSWADHPDASVPEGHYTVPLGKAATVRHGSDVTVLAYGAMVHVAKAGIEESGVDAELLDL 180

Query: 250 RSLLPLDLETIVQSAKKTGRCVVVHEATLTSGFGAELAALVQEHCFYHLESPVVRLTGWD 309
           RS++PLD++ IVQS KKTGRCV++HEA+   GFG EL+ALVQE CFYHL+SP+ R+ GWD
Sbjct: 181 RSIVPLDIDAIVQSVKKTGRCVILHEASRYGGFGGELSALVQERCFYHLKSPIERVAGWD 240

Query: 310 TPYPHAQEWDYFPGPARVGRALAEAM 335
           TPYPHA EWDYFPGP R+ +AL ++M
Sbjct: 241 TPYPHAFEWDYFPGPMRLAKALQKSM 266


Lambda     K      H
   0.321    0.138    0.424 

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: 385
Number of extensions: 13
Number of successful extensions: 1
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: 337
Length of database: 268
Length adjustment: 27
Effective length of query: 310
Effective length of database: 241
Effective search space:    74710
Effective search space used:    74710
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: 48 (23.1 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:

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