GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctP in Desulfovibrio vulgaris Miyazaki F

Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate 8501198 DvMF_1932 TRAP dicarboxylate transporter, DctP subunit (RefSeq)

Query= SwissProt::P37735
         (333 letters)



>FitnessBrowser__Miya:8501198
          Length = 335

 Score =  132 bits (333), Expect = 9e-36
 Identities = 99/321 (30%), Positives = 144/321 (44%), Gaps = 24/321 (7%)

Query: 10  LVGATALSLALSVPALAEPIVIKFSHVVAPDTPKGKGAA----KFEELAEKYTNGAVDVE 65
           LV A  +++AL+ P  A     K    +A  TP G        KF +L  + + G + V+
Sbjct: 7   LVAALLMTVALAAPVQAAYDGPKIKFRLAHTTPPGNHITLAYQKFADLVAEKSGGKITVQ 66

Query: 66  VYPNSQLYKDKEELEALQLGAVQM---LAPSLAKFGPLGVQDFEVFDLPYIFKDYEALHK 122
           V+PN+ L  D+  +E  Q G +++     P+LA F  L    + VFDLPYI       + 
Sbjct: 67  VFPNAILGSDRVLVEGAQKGTLEIGVSSTPNLANFSKL----YSVFDLPYITSPKFQKNL 122

Query: 123 VTQGEAGKML----LSKLEAKGITGLAFWDNGFK-IMSANTPLTMPDDFLGLKMRIQSSK 177
            +  + G  L    L      G+  + + + G++  +S   PL    D  GLKMR   S 
Sbjct: 123 YSAIDPGGTLYDYFLKVANDVGLQPIMYAEYGYRHFVSVKRPLGKASDLAGLKMRTTDSP 182

Query: 178 VLEAEMNALGAVPQVMAFSEVYQALQTGVVDGTENPPSNMFTQKMNEVQKHATVSNHGYL 237
           V      AL   P  +A+ EVY ALQ G +D   N   ++F  K +EV K+A  S H Y 
Sbjct: 183 VEVGVAKALNTNPSPIAWGEVYTALQQGTIDAEGNTFPHLFGAKHHEVLKYAITSAHNYC 242

Query: 238 GYAVIVNKQFWDGLPADVRTGLEKAMAESTDYANGIAKEENEKALQ--------AMKDAG 289
               + NK +WDGLP   +  +  A  E+T Y   +   ENEKA +         + DA 
Sbjct: 243 MQVAMANKAWWDGLPDAAKQVINAAAREATQYQRDVLYPENEKAAREGFIKAGITIHDAT 302

Query: 290 TTEFHELTAEERAAWEEVLTP 310
             E  E     R  W+ V  P
Sbjct: 303 DAEIDEFRKLTRPVWDTVTLP 323


Lambda     K      H
   0.314    0.130    0.364 

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: 236
Number of extensions: 13
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: 333
Length of database: 335
Length adjustment: 28
Effective length of query: 305
Effective length of database: 307
Effective search space:    93635
Effective search space used:    93635
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 (22.0 bits)
S2: 49 (23.5 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