GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03040 in Cupriavidus basilensis 4G11

Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate RR42_RS16445 RR42_RS16445 hypothetical protein

Query= reanno::pseudo3_N2E3:AO353_03040
         (254 letters)



>FitnessBrowser__Cup4G11:RR42_RS16445
          Length = 252

 Score =  242 bits (617), Expect = 6e-69
 Identities = 121/251 (48%), Positives = 177/251 (70%)

Query: 4   LEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLN 63
           ++V+DL+K + + + L GV+L+   G+V+ +IG SGSGKST LR IN LE+P  G I ++
Sbjct: 2   IDVRDLYKHFDAVKALNGVNLEVQRGEVVCLIGPSGSGKSTLLRSINYLERPTRGDISID 61

Query: 64  NEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMSK 123
            + +  V       +    ++L R+RS + MVFQ F LW H++ +EN+    V V G+  
Sbjct: 62  GQTVGHVNQAGKKARPMSGRELARVRSEVGMVFQMFYLWPHLSVLENVTLGMVEVRGVRL 121

Query: 124 AEAREKAELYLAKVGVSHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPE 183
           A+A ++    LAKVG+S + DAYP  +SGG++QRVAIARALAM+P+++LFDEPTSALDPE
Sbjct: 122 ADAAQRGRQLLAKVGLSGKYDAYPEQLSGGQRQRVAIARALAMDPKIILFDEPTSALDPE 181

Query: 184 LVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQSE 243
            VG+VL+ M+ +A EG TM+V THEMGFAR V++++VF+ +G V E+G+P ++   PQS 
Sbjct: 182 RVGEVLQTMETVAAEGMTMIVATHEMGFARRVADRVVFMDEGRVVEAGSPGDIFDRPQSA 241

Query: 244 RLQQFLSGSLK 254
           RL+QFL   L+
Sbjct: 242 RLKQFLDKVLQ 252


Lambda     K      H
   0.317    0.131    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: 5
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: 254
Length of database: 252
Length adjustment: 24
Effective length of query: 230
Effective length of database: 228
Effective search space:    52440
Effective search space used:    52440
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.

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