GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA1 in Magnetospirillum magneticum AMB-1

Align L-rhamnose-1-dehydrogenase; EC 1.1.1.173 (characterized)
to candidate WP_011382728.1 AMB_RS01425 bifunctional aldolase/short-chain dehydrogenase

Query= SwissProt::A3LZU7
         (258 letters)



>NCBI__GCF_000009985.1:WP_011382728.1
          Length = 679

 Score = 95.5 bits (236), Expect = 3e-24
 Identities = 82/256 (32%), Positives = 123/256 (48%), Gaps = 25/256 (9%)

Query: 8   KVVAITGGVTGIGRAIAIEMARNGAKVVVNHLPSEEQAQLAKELKEEISDGENNVLTIPG 67
           +VV +TGG +GIG A A   A+ GA+V V    ++  A+ AK             L I  
Sbjct: 431 QVVVVTGGGSGIGAATAKAFAKEGAEVAVLDRDADAAAKAAKACG-------GKALGIAC 483

Query: 68  DISLPETGRRIVELAVEKFGEINVFVSNAGVCGFREFLEITPETLFQTVNINLNGAFFAI 127
           D++ P + R   +   E+FG ++V VSNAG        E+   TL  +  +N    FF  
Sbjct: 484 DVTDPASVRAAFDRVAERFGGVDVVVSNAGAAWQGAVGEVDDSTLRASFELN----FFGH 539

Query: 128 QAAAQQMVK----QGKGGSIIGISSISALVGGAHQTHYTPTKAGILSLMQSTACALGKYG 183
           QA AQ  V+    QG GG+++  +S  A+  G +   Y   KA  L LM+  A   GK G
Sbjct: 540 QAVAQNAVRVFKAQGTGGALLFNASKQAVNPGKNFGPYGLPKAATLFLMKQYALDHGKDG 599

Query: 184 IRCNAILPGTISTALNEEDL-------KDPEKRKYMEGRIPLGRVGDPKDIAGPAIFLAS 236
           IR NA+    I + L  +D+       +   ++ YM G + LGR    +D+A   ++LA 
Sbjct: 600 IRSNAVNADRIRSGLLTDDMIKSRSSARGLSEQDYMGGNL-LGREVTAEDVADAFVWLAK 658

Query: 237 DMSNYVNGAQLLVDGG 252
             ++ V    + VDGG
Sbjct: 659 --ASKVTACTVTVDGG 672


Lambda     K      H
   0.317    0.136    0.382 

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: 300
Number of extensions: 16
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: 258
Length of database: 679
Length adjustment: 31
Effective length of query: 227
Effective length of database: 648
Effective search space:   147096
Effective search space used:   147096
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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