GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03040 in Cereibacter sphaeroides ATCC 17029

Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate WP_172599875.1 RSPH17029_RS02015 amino acid ABC transporter ATP-binding protein

Query= reanno::pseudo1_N1B4:Pf1N1B4_3435
         (254 letters)



>NCBI__GCF_000015985.1:WP_172599875.1
          Length = 249

 Score =  234 bits (596), Expect = 2e-66
 Identities = 119/247 (48%), Positives = 166/247 (67%), Gaps = 11/247 (4%)

Query: 4   LEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLN 63
           +++  ++K YGS  VL+ V++    G+ I I G SGSGKST +RCIN LE+  +G+I+++
Sbjct: 9   IQISQMNKWYGSFHVLRDVNMTVHKGERIVICGPSGSGKSTLIRCINRLEEHQSGQIVVD 68

Query: 64  NEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMSK 123
             EL            +D K + ++RS + MVFQHFNL+ H+T +EN   AP+ V    K
Sbjct: 69  GIEL-----------TSDLKNIDKVRSEVGMVFQHFNLFPHLTILENCTLAPIWVRKTPK 117

Query: 124 TEAREKAEHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPE 183
            EA E A HYL KV +  +   YPG +SGG+QQRVAIAR+L M+P +MLFDEPTSALDPE
Sbjct: 118 KEAEEVAMHYLKKVKIPEQAHKYPGQLSGGQQQRVAIARSLCMKPRIMLFDEPTSALDPE 177

Query: 184 LVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQSE 243
           ++ +VL  M  LA+EG TM+ VTHEMGFA+ V+N+++F+ +G + E   P E   NP+SE
Sbjct: 178 MIKEVLDTMIELAEEGMTMLCVTHEMGFAQAVANRVIFMDQGQIVEQNEPGEFFRNPKSE 237

Query: 244 RLQQFLS 250
           R + FLS
Sbjct: 238 RTKLFLS 244


Lambda     K      H
   0.317    0.131    0.366 

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: 181
Number of extensions: 10
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: 254
Length of database: 249
Length adjustment: 24
Effective length of query: 230
Effective length of database: 225
Effective search space:    51750
Effective search space used:    51750
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 Apr 09 2024. 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