GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatP in Desulfovibrio vulgaris Hildenborough

Align ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized)
to candidate 206179 DVU0753 amino acid ABC transporter, ATP-binding protein

Query= reanno::pseudo13_GW456_L13:PfGW456L13_4773
         (244 letters)



>MicrobesOnline__882:206179
          Length = 243

 Score =  292 bits (748), Expect = 4e-84
 Identities = 147/245 (60%), Positives = 184/245 (75%), Gaps = 3/245 (1%)

Query: 1   MISIKSINKWY-GDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDIV 59
           MI  + ++KWY     VL D + ++ +GEV+V+CGPSGSGKSTLI+C+N LE  QKG+IV
Sbjct: 1   MIHFEHVHKWYPSGLHVLNDINLDIAQGEVVVICGPSGSGKSTLIRCINRLEAIQKGNIV 60

Query: 60  VDGTSIADPKTNLPKLRSRVGMVFQHFELFPHLTITENLTIAQIKVLGRSKEEATKKGLQ 119
           VDG  I  P+TNL  LR+ VG VFQ F L+PH+T+ EN+T+A   V    + EA +  ++
Sbjct: 61  VDGIDINAPRTNLTLLRAEVGFVFQQFNLYPHMTVLENITLAPTLVRNIPRAEAERTAME 120

Query: 120 LLERVGLSAHAHKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVNEVLDVM 179
           LLE+V +   A  +PGQLSGGQQQRVAIAR LAM P +MLFDEPTSALDPEM+NEVLDVM
Sbjct: 121 LLEKVNIPDKAGAYPGQLSGGQQQRVAIARGLAMKPRIMLFDEPTSALDPEMINEVLDVM 180

Query: 180 VQLAHEGMTMMCVTHEMGFARKVADRVIFMDQGKIIEDCKKEEFFGDINARAERTQHFLN 239
            QLA EGMTM+CVTHEMGFAR+VADRVIFMDQG ++E    + FF   N + ER++ FL+
Sbjct: 181 RQLAREGMTMVCVTHEMGFAREVADRVIFMDQGILVEQNTPDAFFN--NPQHERSREFLS 238

Query: 240 KILQH 244
           KIL H
Sbjct: 239 KILTH 243


Lambda     K      H
   0.321    0.136    0.394 

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: 218
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: 244
Length of database: 243
Length adjustment: 24
Effective length of query: 220
Effective length of database: 219
Effective search space:    48180
Effective search space used:    48180
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 (21.9 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