GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacB in Lactobacillus pobuzihii E100301

Align L-arabinose 1-dehydrogenase (EC 1.1.1.46) (characterized)
to candidate WP_017868407.1 LACPOB_RS0108455 SDR family oxidoreductase

Query= reanno::ANA3:7024897
         (256 letters)



>NCBI__GCF_000349725.1:WP_017868407.1
          Length = 242

 Score =  122 bits (306), Expect = 7e-33
 Identities = 84/252 (33%), Positives = 121/252 (48%), Gaps = 19/252 (7%)

Query: 10  LQGKTIFISGGATGIGACLVNAFLEQGAKVAFVDILVEESTQLVADLKQTQPEA-----S 64
           +  + I I+G A+G+      AFLEQG  V   D   +        LKQ +  A     S
Sbjct: 1   MASRNIIITGAASGMAKAQTEAFLEQGDTVFGFDFNEQ-------GLKQEEQNAGAFKGS 53

Query: 65  VTFYHCDLVDIAALKRVIAQVEDDLGPISVLINNAAC-DQRHSIDEVTPEYWDQCLNTNL 123
              Y  D+     +   +  V + +  I VLIN A   D+     E T E WD  LNTNL
Sbjct: 54  FYGYKVDISSKIQIDNALKNVWEKVDRIDVLINTAGIFDKYQKFLETTEEMWDAVLNTNL 113

Query: 124 RHYFFAVQAVRPQMQRLGGGSVINLGSMSWHNRQAGMAGYTASKAGAMGLTRGLAADLGK 183
           +  F   QAV  +M + GGG+VIN+ S++   +  G   YT +K G +GLT+ ++ +LG 
Sbjct: 114 KGMFLLTQAVTAKMIKNGGGNVINVASVAGLQQDGGGVAYTVAKHGVIGLTKKISYELGT 173

Query: 184 DKIRINTLTPGWVMTKRQLTHWVDKDTAKHIENNQCIKEYVMPEDIAAMALFLAADDSKL 243
             IR+N + PG + T       ++ +T+  I +N   +     EDI    LFLA+D S  
Sbjct: 174 QGIRVNAIAPGRITTN------MNNNTSDLIVDNLPAQRNGKVEDIVNATLFLASDKSSY 227

Query: 244 CTAQNFIVDGGW 255
              Q   VDGGW
Sbjct: 228 IHGQVITVDGGW 239


Lambda     K      H
   0.320    0.134    0.406 

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: 160
Number of extensions: 9
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: 256
Length of database: 242
Length adjustment: 24
Effective length of query: 232
Effective length of database: 218
Effective search space:    50576
Effective search space used:    50576
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: 46 (22.3 bits)

This GapMind analysis is from Sep 24 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