GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treV in Desulfovibrio vulgaris Miyazaki F

Align TreV, component of Trehalose porter (characterized)
to candidate 8499890 DvMF_0655 ABC transporter related (RefSeq)

Query= TCDB::Q97ZC0
         (324 letters)



>FitnessBrowser__Miya:8499890
          Length = 350

 Score =  221 bits (564), Expect = 2e-62
 Identities = 115/310 (37%), Positives = 186/310 (60%), Gaps = 17/310 (5%)

Query: 3   VELIDIVKKYGKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKIIAD 62
           ++L+++ + +G    ++ ++ ++E G   V+LGPSG GKST L+++AG+E +  G+I+  
Sbjct: 4   IQLLNVSRHWGDVRAVDDVSFEVEQGTMLVLLGPSGCGKSTTLRLIAGLESVTSGRIMIG 63

Query: 63  GADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLLGI 122
             D+T  PP +R +AMVFQ+YAL+P+++VR+NI F L +R + + E  +R+ +A  +LG+
Sbjct: 64  ERDVTHLPPAQRQLAMVFQSYALFPHLTVRENILFGLTVRKVPEAEREKRLTRAVDILGL 123

Query: 123 SEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQKEL 182
           S +L +K  ++SGGQQQRVAL RA+V   +  L+DEPLSNLDA++R   R E++ +Q+ L
Sbjct: 124 SALLQRKPGELSGGQQQRVALGRALVAEAAVCLMDEPLSNLDAKLRHEMRREIRALQQTL 183

Query: 183 KGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMNFL- 241
             T +YVTHDQ EA+S+ADRI ++  G+  Q + P  LY  P T +   F+G  PMN + 
Sbjct: 184 GMTMVYVTHDQTEAMSMADRIILMQGGRIVQNATPSELYSRPATTFAGNFIGTPPMNLVR 243

Query: 242 ----------------PGELMKEKAQEIGFRPEWVEVGKGNLSCMVESVEASGESRYLIC 285
                              ++      +G RPE + +       +VESVE  G    L C
Sbjct: 244 LDDARGSVCVAGSRSGTVSVVDSADYVLGIRPEHIRIVPEGWRAVVESVEYLGSGSVLGC 303

Query: 286 NFKNNNITIL 295
                 ++++
Sbjct: 304 RVGGEELSVV 313


Lambda     K      H
   0.318    0.137    0.385 

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: 224
Number of extensions: 3
Number of successful extensions: 2
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: 324
Length of database: 350
Length adjustment: 28
Effective length of query: 296
Effective length of database: 322
Effective search space:    95312
Effective search space used:    95312
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: 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