GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA1 in Halococcus hamelinensis 100A6

Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_007691607.1 C447_RS05270 SDR family oxidoreductase

Query= metacyc::MONOMER-16230
         (256 letters)



>NCBI__GCF_000336675.1:WP_007691607.1
          Length = 253

 Score =  155 bits (391), Expect = 1e-42
 Identities = 102/250 (40%), Positives = 143/250 (57%), Gaps = 11/250 (4%)

Query: 6   KTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTAIAVGA 65
           KTV +TGA  GIGRA A  CA +GA VV+    +D  R G     E IA  GG A     
Sbjct: 6   KTVFITGAGAGIGRATAERCADEGATVVV----TDVDREGGEETVERIADAGGEATFHEL 61

Query: 66  DAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLD-MPRELYLKTVGTNLNGAYFT 124
           D +D D+ E  V   V+  G +DV+VNNAGI    + ++      + + +  NL G +  
Sbjct: 62  DVSDADAFEDCVDTVVDEHG-LDVVVNNAGIGHAPAAVEETDTRTFERVLDVNLRGVWNG 120

Query: 125 VQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPYGIRC 184
             AA   +K Q   GAI+ V S+++L+G   Q+ Y+ TK  +L+  ++ A   GP+ +R 
Sbjct: 121 CHAALPVLKAQ-ESGAIVNVGSLASLLGLPKQSVYSLTKGAVLNFTRAVAAEAGPHDVRA 179

Query: 185 NAVLPGTIATDINKEDLS---DLEKR-ERMTSRVPLGRLGEPDDLAGPIVFLASDMARYV 240
           NAV PG   T + ++  +   D EK  ERMT++ PL RLGEP+++AG I FLAS+ A YV
Sbjct: 180 NAVCPGFTDTQLGQQYFASQGDPEKAIERMTAQYPLRRLGEPEEVAGCIAFLASEDASYV 239

Query: 241 TGASLLVDGG 250
           TG  L+VDGG
Sbjct: 240 TGQGLVVDGG 249


Lambda     K      H
   0.319    0.136    0.383 

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: 189
Number of extensions: 16
Number of successful extensions: 5
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: 253
Length adjustment: 24
Effective length of query: 232
Effective length of database: 229
Effective search space:    53128
Effective search space used:    53128
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: 47 (22.7 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