GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA1 in Klebsiella michiganensis M5al

Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate BWI76_RS07640 BWI76_RS07640 short chain dehydrogenase

Query= metacyc::MONOMER-16231
         (254 letters)



>FitnessBrowser__Koxy:BWI76_RS07640
          Length = 261

 Score =  147 bits (372), Expect = 2e-40
 Identities = 94/247 (38%), Positives = 135/247 (54%), Gaps = 4/247 (1%)

Query: 4   LEGKTVLVTGASTGIGRAAAIGAAQHGADVAINYAHSDGPAQSCVAEIEALGQRAIAVKG 63
           L+ +   VTGA +GIG+  A G A  GA V       DG     V  IEA+G  A    G
Sbjct: 13  LQDRVAFVTGAGSGIGQMIAYGLASAGARVVCFDLREDGGLAETVKNIEAIGGEACFYTG 72

Query: 64  DVADPQTAQDFVAKAVETFGKVDVMVSNAGICPFHAFLDMPVDVVERTFKVNLHGAYFMV 123
           DV      +  VA A   FG++D+ V+ AGI   +  L+M  +  +R   +NL G +   
Sbjct: 73  DVRQLSDLRAGVALAKSRFGRLDIAVNAAGIANANPALEMETEQWQRVIDINLTGVWNSC 132

Query: 124 QAAAQQMVRQGHGGSIVAVSSISALV--GGEYQTHYTPTKAGVHSLMQSTAIALGKHGIR 181
           +A A+ M   G GGSI+ ++S+S ++   G  Q HY  +KAGV  L +S A+     GIR
Sbjct: 133 KAEAELMQETG-GGSIINIASMSGIIVNRGLDQAHYNCSKAGVIHLSKSLAMEWIGKGIR 191

Query: 182 CNSVLPGTILTEINKDDLADQEKREYMEARTPLGRLGAPEDLAGPIVFLASDMAAYVTGA 241
            NS+ PG   T +N       + RE+ E++TP+ R+   E++AGP +FLASD A++ TG 
Sbjct: 192 VNSISPGYTATPMNTRPEMVHQTREF-ESQTPIQRMAKVEEMAGPALFLASDAASFCTGV 250

Query: 242 ALLVDGG 248
            L+VDGG
Sbjct: 251 DLVVDGG 257


Lambda     K      H
   0.318    0.133    0.379 

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: 123
Number of extensions: 5
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: 254
Length of database: 261
Length adjustment: 24
Effective length of query: 230
Effective length of database: 237
Effective search space:    54510
Effective search space used:    54510
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 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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