GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltI in Desulfovibrio vulgaris Hildenborough

Align ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, periplasmic substrate-binding component (characterized)
to candidate 206178 DVU0752 amino acid ABC transporter, amino acid-binding protein

Query= reanno::pseudo3_N2E3:AO353_16290
         (304 letters)



>MicrobesOnline__882:206178
          Length = 275

 Score =  112 bits (281), Expect = 7e-30
 Identities = 83/267 (31%), Positives = 126/267 (47%), Gaps = 16/267 (5%)

Query: 11  AITAALISTPVFAAELTGTLKKIKESGTITLGHRDASIPFSYIADASGVPVGYSHDIQLK 70
           A+ AA +     AA        + +   I +G    SIP  +  +  G   G+ +DI  +
Sbjct: 8   ALAAAFLVFTGSAALAGPAYDNVMKDKKIRVGLMTDSIPGGFYNE-KGEWGGFDYDIATE 66

Query: 71  IVEAIKKDLDMPNLKVKYNLVTSQTRIPLVQNGTVDVECGSTTNNTERQQQVDFSVGIFE 130
           I + +  D++          V ++TRI  VQ G VD+   + T+  ER + VDFS+  F 
Sbjct: 67  IAKRMGVDIERVQ-------VNNKTRIAYVQQGRVDISVSNMTHTRERDKSVDFSITYFF 119

Query: 131 IGTKLLSKKDSTYKDFADLKGKNVVTTAGTTSE----RILKSMNADKQMGMNVISAKDHG 186
            G K+L+KK   +K   D+ GK + T  GTTSE    R LK    D     +VIS +   
Sbjct: 120 DGQKVLAKK-GQFKSVKDMVGKKIATMQGTTSEVNVKRALKEA-GDPNPDQSVISFQKES 177

Query: 187 ESFQMLESGRAVAFMMDDALLAGEMAKAKSPTDWAVTGTAQSYEIYGCMVRKGDAPFKKA 246
           E FQ L+ GR   +  D ++L G    AK P  + + G   + E YG  + + D+  + A
Sbjct: 178 ECFQALQMGRVAGWSTDASILVG--YSAKEPGKFELVGNFLAEEPYGIAMPQDDSALRDA 235

Query: 247 VDDAIVATYKSGEINTIYGKWFTQPIP 273
           V+ A+   +K G   TIY KW+    P
Sbjct: 236 VNAALQDMWKDGTYKTIYNKWYGPGTP 262


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: 189
Number of extensions: 16
Number of successful extensions: 4
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: 304
Length of database: 275
Length adjustment: 26
Effective length of query: 278
Effective length of database: 249
Effective search space:    69222
Effective search space used:    69222
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: 42 (22.0 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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