GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03040 in Flavobacterium ummariense DS-12

Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate WP_091525598.1 BM253_RS14120 ATP-binding cassette domain-containing protein

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



>NCBI__GCF_900115115.1:WP_091525598.1
          Length = 254

 Score =  122 bits (306), Expect = 7e-33
 Identities = 74/235 (31%), Positives = 120/235 (51%), Gaps = 11/235 (4%)

Query: 4   LEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLN 63
           +EV+DL K +   EVLKG++    AG    IIG SGSGK+  L+ +  +  P +G+IL +
Sbjct: 2   IEVKDLKKSFDDKEVLKGITTTYEAGKTNLIIGQSGSGKTVMLKTLLGVHIPDSGQILFD 61

Query: 64  NEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMSK 123
             +   +          DP + + +R+ + MVFQ   L+  M   ENI          S 
Sbjct: 62  GRDFATL----------DPNEKRTLRTEMGMVFQGSALFDSMNVEENIGFPLKMFTKKSN 111

Query: 124 TEAREKAEHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPE 183
            E R++ +  +++V +       P  +SGG Q+RVAIARA+   P+ +  DEP S LDP+
Sbjct: 112 AEIRDRVQEVIDRVKLIDANKKMPSEISGGMQKRVAIARAIVNNPKYLFCDEPNSGLDPK 171

Query: 184 LVGDVLKVMQALAQE-GRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVL 237
               + +++Q +  E   T V+ TH+M    ++   + FL  G +   GN  E++
Sbjct: 172 TSIVIDELIQEITHEYNITTVINTHDMNSVLQIGEHICFLKDGKLVWEGNSEEIM 226


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: 153
Number of extensions: 12
Number of successful extensions: 4
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: 254
Length adjustment: 24
Effective length of query: 230
Effective length of database: 230
Effective search space:    52900
Effective search space used:    52900
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