GapMind for catabolism of small carbon sources

 

Alignments for a candidate for peb1C in Desulfovibrio vulgaris Hildenborough

Align PEB1C, component of Uptake system for glutamate and aspartate (characterized)
to candidate 206675 DVU1236 amino acid ABC transporter, ATP-binding protein

Query= TCDB::A3ZI83
         (242 letters)



>MicrobesOnline__882:206675
          Length = 247

 Score =  251 bits (641), Expect = 9e-72
 Identities = 134/241 (55%), Positives = 172/241 (71%), Gaps = 2/241 (0%)

Query: 1   MIELKNVNKYYGTHHVLKNINLSVKEGEKLVIIGPSGSGKSTTIRCMNGLEEVSSGEVVV 60
           +I ++NV K++G    L +++L V+ GEK+VIIGPSGSGKST +R +N LE V  G ++V
Sbjct: 8   IISIRNVWKFFGELTALHDVSLDVQAGEKVVIIGPSGSGKSTLLRSINRLENVDKGSIIV 67

Query: 61  NNLVLNHKNK-IEICRKYCAMVFQHFNLYPHMTVLQNLTLAPMKLQKKSKKEAEETAFKY 119
           +   +  ++  I + R+   MVFQ FNL+PH TVLQNLT+APM+L+K  + EAE  A   
Sbjct: 68  DGKDIRAEDSDINVIRQDLGMVFQSFNLFPHKTVLQNLTMAPMRLRKVPRDEAESRALDL 127

Query: 120 LKVVGLLDKANVYPATLSGGQQQRVAIARSLCTKKPYILFDEPTSALDPETIQEVLDVMK 179
           LK VG+ DKANVYPA LSGGQQQRVAIAR+L      +LFDEPTSALDPE I EVLDVM 
Sbjct: 128 LKKVGISDKANVYPAMLSGGQQQRVAIARALAMNPKIMLFDEPTSALDPEMIGEVLDVMV 187

Query: 180 EISHQSNTTMVVVTHEMGFAKEVADRIIFMEDGAIVEENIPSEFFSNPKTERARLFLGKI 239
            ++ +   TMV VTHEMGFA+EVADRIIFM+ G I+E+  P  FF  P+  R + FL +I
Sbjct: 188 TLA-KEGMTMVCVTHEMGFAREVADRIIFMDHGQILEQGTPQHFFEAPEHPRLQKFLQQI 246

Query: 240 L 240
           L
Sbjct: 247 L 247


Lambda     K      H
   0.317    0.133    0.372 

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: 168
Number of extensions: 3
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: 242
Length of database: 247
Length adjustment: 24
Effective length of query: 218
Effective length of database: 223
Effective search space:    48614
Effective search space used:    48614
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: 46 (22.3 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