GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03040 in Brucella inopinata BO1

Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate WP_008511698.1 BIBO1_RS20000 amino acid ABC transporter ATP-binding protein

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



>NCBI__GCF_000182725.1:WP_008511698.1
          Length = 263

 Score =  241 bits (615), Expect = 1e-68
 Identities = 121/247 (48%), Positives = 168/247 (68%), Gaps = 11/247 (4%)

Query: 4   LEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLN 63
           +E++++HK YG   VL+ ++LK   G+ I + G SGSGKST +RC+N LE+   G+I+++
Sbjct: 24  IEIKNMHKWYGEFHVLRDINLKVMRGERIVVAGPSGSGKSTMIRCVNRLEEHQKGQIIVD 83

Query: 64  NEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMSK 123
             EL             D K++  +R  + MVFQHFNL+ H+T +EN   AP+ V  M K
Sbjct: 84  GIEL-----------TNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVRKMPK 132

Query: 124 TEAREKAEHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPE 183
            +A E A HYL +V +  + + YPG +SGG+QQRVAIARAL M P+VMLFDEPTSALDPE
Sbjct: 133 KQAEEIAMHYLERVKIPEQANKYPGQLSGGQQQRVAIARALCMSPKVMLFDEPTSALDPE 192

Query: 184 LVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQSE 243
           +V +VL  M +LA EG TM+ VTHEMGFAR+V+N+++F+ +G + E  +P E   NPQ E
Sbjct: 193 MVKEVLDTMVSLAAEGMTMICVTHEMGFARQVANRVIFMDQGQIVEQNSPDEFFDNPQHE 252

Query: 244 RLQQFLS 250
           R + FLS
Sbjct: 253 RTKLFLS 259


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: 191
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: 263
Length adjustment: 24
Effective length of query: 230
Effective length of database: 239
Effective search space:    54970
Effective search space used:    54970
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: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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