GapMind for catabolism of small carbon sources

 

Alignments for a candidate for srlD in Catellicoccus marimammalium M35/04/3

Align sorbitol-6-phosphate dehydrogenase subunit (EC 1.1.1.140) (characterized)
to candidate WP_009489301.1 C683_RS02490 3-oxoacyl-ACP reductase

Query= metacyc::MONOMER-13092
         (266 letters)



>NCBI__GCF_000313915.1:WP_009489301.1
          Length = 242

 Score =  105 bits (261), Expect = 1e-27
 Identities = 79/253 (31%), Positives = 120/253 (47%), Gaps = 24/253 (9%)

Query: 10  KTVIVTGASSGIGKAIVDELLSLKVKVANFDLTDNGEKHENLLFQKVDVTSREQVEASVA 69
           ++V++TG SSGIGKA  +  L     V   D      +H N  F   D+T  ++VE    
Sbjct: 9   QSVVITGCSSGIGKAQAEAFLDKGAMVYGLDCQPCPLEHPNFFFSLCDITKEKEVEK--- 65

Query: 70  AVVEHFGTVDAVVNNAGINIPRLLVDPKDPHGQYELDDATFEKITMINQKGLYLVSQAVG 129
            V++    VD + N AGI      +D   P     ++   F++I  +N +G +L+  A  
Sbjct: 66  -VLQKIERVDILCNTAGI------LDDFAPSLDTSVE--LFDRIFAVNVRGTFLLCNACL 116

Query: 130 RLLVAKKKGVIINMASEAGLEGSEGQSAYAGTKAAVYSYTRSWAKELGKYGVRVVGIAPG 189
             ++A+ KG IINMAS A L    G +AY  +K A+Y YT+    +  + G+R   IAPG
Sbjct: 117 PKMLAQGKGCIINMASIASLIPGGGGAAYTASKHAIYGYTKQLTYDYARKGIRANAIAPG 176

Query: 190 IMEATGLRTLAYEEALGYTRGKTVEEIRAGYASTTTTPLGRSGKLSEVADLVAYYISDRS 249
                 +RT   ++      G+  +EI         TP GR  +  E+A +  +  SD +
Sbjct: 177 -----AIRTPMNQKDF-LNGGEIAKEI------AKETPCGRYAEPEEIAQVTLFLASDDA 224

Query: 250 SYITGITTNVAGG 262
            YI G    V GG
Sbjct: 225 RYIYGDIIPVDGG 237


Lambda     K      H
   0.313    0.131    0.361 

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: 147
Number of extensions: 7
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: 266
Length of database: 242
Length adjustment: 24
Effective length of query: 242
Effective length of database: 218
Effective search space:    52756
Effective search space used:    52756
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 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