GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lhgD in Sinorhizobium meliloti 1021

Align (S)-2-hydroxyglutarate oxidase (characterized)
to candidate SM_b20101 SM_b20101 hydroxyglutarate oxidase

Query= metacyc::G1G01-3089-MONOMER
         (416 letters)



>FitnessBrowser__Smeli:SM_b20101
          Length = 426

 Score =  411 bits (1056), Expect = e-119
 Identities = 207/394 (52%), Positives = 267/394 (67%)

Query: 1   MYDFIIIGGGIVGMSTAMHLIKVYPDAKMLLLEKESGPARHQTGHNSGVIHAGVYYTPGS 60
           +YD+ IIGGGIVG++TAM L +    A ++LLEKE   ARHQTGHNSGVIHAG+YY PGS
Sbjct: 12  LYDYCIIGGGIVGLATAMALQERMGGASIVLLEKERELARHQTGHNSGVIHAGIYYAPGS 71

Query: 61  LKARFCLEGNKATKAFCTQHGIRFDECGKLLVATNDLEMQRMKALWERTAANGLERYWLS 120
           LKA+ C EG +ATK FCT +GI F+ CGKLLVATND E++RM++L ER   NG+E   LS
Sbjct: 72  LKAKLCREGAEATKEFCTGNGISFETCGKLLVATNDAEIERMESLEERAQQNGIEYTRLS 131

Query: 121 ADELREREPNIVGMGGIFVPSSGIVNYAQVTAAMAAEFQRAGGEIRYGAEVVGLQEQANE 180
             +LR  EPNI G+  + V ++GIV+Y+ V  AMA   +  GGEIR G E   + E+   
Sbjct: 132 KSQLRSDEPNIAGLSALLVHATGIVDYSAVCRAMAERIEVRGGEIRCGVEATAIAEEDGG 191

Query: 181 VIVRTQRDELHSRFLVTCSGLMADRVVGMLGLRTEFVICPFRGEYYLLPKQHNQIVNHLI 240
           V + +    + +R L+ C+GL +DR+  M GL  +  I PFRGEYY+LP     +   LI
Sbjct: 192 VRIASATGRIEARRLIACAGLQSDRIALMAGLSIDHRIVPFRGEYYVLPASKAGVTRRLI 251

Query: 241 YPIPDPSMPFLGVHLTRMIDGTVTVGPNAVLAMKREGYRKTDVSPSDLFQTLTTPGILKV 300
           YPIPDP++PFLG+HLTR IDG +TVGPNAVL   REGY K     +D+      PG  K+
Sbjct: 252 YPIPDPNLPFLGIHLTRTIDGGMTVGPNAVLGFAREGYPKGSFKAADVANMAAFPGFWKM 311

Query: 301 LAKNFRPGLIEMKNSLFKGGYLKQVQKYCPSIIKADLTPYPAGVRAQAVSRDGKLIDDFL 360
            AKN+R  + E  NS  +  YL++ +KYCPS+   DL    AG+RAQAV  DG L+ DFL
Sbjct: 312 AAKNWRSAITEFANSASRFRYLRECRKYCPSLTIDDLAVPQAGIRAQAVMADGSLVHDFL 371

Query: 361 FVNTARSVNVCNAPSPAATSAIPIGAYIVEKVCE 394
           F  T R ++VCNAPSPAATSAIPIG  IV+++ +
Sbjct: 372 FKQTERMLHVCNAPSPAATSAIPIGRMIVDRLLD 405


Lambda     K      H
   0.321    0.137    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: 541
Number of extensions: 24
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: 416
Length of database: 426
Length adjustment: 32
Effective length of query: 384
Effective length of database: 394
Effective search space:   151296
Effective search space used:   151296
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)

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