GapMind for catabolism of small carbon sources

 

Alignments for a candidate for srlD in Methylocystis bryophila S285

Align sorbitol-6-phosphate dehydrogenase (characterized)
to candidate WP_085770280.1 B1812_RS02990 3-oxoacyl-[acyl-carrier-protein] reductase

Query= CharProtDB::CH_091826
         (259 letters)



>NCBI__GCF_002117405.1:WP_085770280.1
          Length = 246

 Score =  114 bits (285), Expect = 2e-30
 Identities = 81/256 (31%), Positives = 129/256 (50%), Gaps = 18/256 (7%)

Query: 3   QVAVVIGGGQTLGAFLCEGLAQAGYHVAVADLNESNANRLADTINSRYGAGRAYGFKVDA 62
           + A+V G    LG  +   L QAG  V ++         LA  +  R     A+    + 
Sbjct: 7   KTALVTGASSGLGLAIARTLHQAGATVGLSGTRREALETLAGELKER-----AHILPCNL 61

Query: 63  TDEASVEALARAVDETFGRADLLVYSAGVAKAAPITQFRLTDFDLSLQVNLVGYFLCSRE 122
           +D A  + L  A +   G  D+LV +AG+ +     + +  D+D  L VNL   F  SR 
Sbjct: 62  SDRAETDKLIPAAEGAMGGVDILVNNAGITRDMLFMRMKDEDWDAVLAVNLTAAFRLSRA 121

Query: 123 FSKLMIRDGIKGRIIQINSKSGKVGSKHNSGYSAAKFGGVGLTQSLALDLAEYGITVHSL 182
             + M+R    GRII I S +G VG+   + YSAAK G  G+T+SLA ++A  G+TV+ +
Sbjct: 122 VLRGMMRKR-HGRIINITSVAGAVGNPGQANYSAAKAGLTGMTKSLANEVASRGVTVNCV 180

Query: 183 MLGNLLKSPMFQSLLPQYAEKLGITPEEVEPYYVDKVPLKRGCDYQDVLNVLLFYASDKA 242
             G +++SPM Q L     E+L           +  +P++R     ++   +L+ ASD+A
Sbjct: 181 APG-VIESPMTQVLNEAQRERL-----------LKLIPMERFGSADEIGAAVLYLASDEA 228

Query: 243 AYCTGQSINVTGGQVM 258
           A+ TGQ++++ GG  M
Sbjct: 229 AFITGQTLHINGGMAM 244


Lambda     K      H
   0.319    0.136    0.387 

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: 161
Number of extensions: 14
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: 259
Length of database: 246
Length adjustment: 24
Effective length of query: 235
Effective length of database: 222
Effective search space:    52170
Effective search space used:    52170
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 (21.7 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Apr 09 2024. 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