GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03040 in Haloterrigena daqingensis JX313

Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate WP_076583323.1 BB347_RS14205 phosphonate ABC transporter ATP-binding protein

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



>NCBI__GCF_001971705.1:WP_076583323.1
          Length = 280

 Score =  137 bits (346), Expect = 2e-37
 Identities = 87/251 (34%), Positives = 136/251 (54%), Gaps = 20/251 (7%)

Query: 4   LEVQDLHKRY-GSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILL 62
           L  Q++ K Y G  E L+GVS      +V++IIG SG+GKST + CIN L +P  G+I L
Sbjct: 2   LTAQNISKTYPGGEEALRGVSFDVTGDEVVAIIGPSGAGKSTLIECINRLTEPTDGEIRL 61

Query: 63  NNEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMS 122
           +          D  + A   +QL+R R  ++M+FQ +NL   +T MEN++   +  L   
Sbjct: 62  D----------DVTVTALSDRQLRRTRRDIAMIFQEYNLVERLTVMENVLSGRLGYLSTW 111

Query: 123 KTEAR-------EKAEHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDE 175
               R       E A   L +VG+   +      +SGG++QRV IARA+   P++ML DE
Sbjct: 112 NAFRRKFPAEDIEFARETLERVGLGGHERDRADELSGGQRQRVGIARAVVQRPKIMLADE 171

Query: 176 PTSALDPELVGDVLKVMQALAQEGRTMVVVT-HEMGFAREVSNQLVFLHKGVVEESGNPR 234
           PTS+LDPE    V++++  +A + R  V++  HE+  A E +++++ L  G +   G P 
Sbjct: 172 PTSSLDPETSHAVMELLTEIAADERIPVLINIHEVELAVEYADRIIGLADGELVFDG-PP 230

Query: 235 EVLVNPQSERL 245
           E L     +R+
Sbjct: 231 EALDETAKDRI 241


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: 185
Number of extensions: 9
Number of successful extensions: 3
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: 280
Length adjustment: 25
Effective length of query: 229
Effective length of database: 255
Effective search space:    58395
Effective search space used:    58395
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