GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03040 in Amantichitinum ursilacus IGB-41

Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate WP_053938866.1 WG78_RS16145 amino acid ABC transporter ATP-binding protein

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



>NCBI__GCF_001294205.1:WP_053938866.1
          Length = 242

 Score =  216 bits (551), Expect = 3e-61
 Identities = 113/248 (45%), Positives = 162/248 (65%), Gaps = 13/248 (5%)

Query: 4   LEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLN 63
           + ++++ K YG  +VL   S +   G+V+ + G SGSGKST ++C+N LE    G I+++
Sbjct: 2   ISIKNISKWYGDFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKCVNGLEAFQKGDIIVD 61

Query: 64  NEELKLVANKDGALKAADPK-QLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMS 122
              +             DPK  L ++RSR+ MVFQ+F L+ H++  +N+  A + VLG +
Sbjct: 62  GTSV------------GDPKTNLPKLRSRVGMVFQNFELFPHLSITQNLTLAQMQVLGRN 109

Query: 123 KTEAREKAEHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDP 182
           + EA       L++VG+    D +PG +SGG+QQRVAIARALAM+P  MLFDEPTSALDP
Sbjct: 110 RDEATVNGLRLLDRVGLKAHADKHPGQLSGGQQQRVAIARALAMDPIAMLFDEPTSALDP 169

Query: 183 ELVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQS 242
           E+V +VL VM  LAQEG TM+ VTHEMGFAR+V+N+++F+ KG + E     +   +P+S
Sbjct: 170 EMVNEVLDVMVELAQEGMTMMCVTHEMGFARKVANRVIFMDKGAIVEDATKEDFFGSPRS 229

Query: 243 ERLQQFLS 250
           ER Q FLS
Sbjct: 230 ERAQVFLS 237


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: 171
Number of extensions: 7
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: 242
Length adjustment: 24
Effective length of query: 230
Effective length of database: 218
Effective search space:    50140
Effective search space used:    50140
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 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