GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02869 in Thiothrix lacustris DSM 21227

Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate WP_028489030.1 Q394_RS0109195 ABC transporter ATP-binding protein

Query= reanno::Phaeo:GFF2754
         (331 letters)



>NCBI__GCF_000621325.1:WP_028489030.1
          Length = 348

 Score =  339 bits (870), Expect = 5e-98
 Identities = 181/339 (53%), Positives = 239/339 (70%), Gaps = 8/339 (2%)

Query: 1   MTALQLTNVCKSFGPVEVLKDINLTVEDGEFVVFVGPSGCGKSTLLRVISGLEDATAGEI 60
           M  L+L NV K +G +  +K ++L ++ GEF+VFVGPSGCGKSTLLR+I+GLE    G++
Sbjct: 1   MAFLELKNVDKYYGKLHAIKQVSLEIQSGEFIVFVGPSGCGKSTLLRMIAGLEVINGGQL 60

Query: 61  SIGGQTVTTTPPAKRGIAMVFQSYALYPHLSVRENMALALKQERQPKEEIAARVAEASRM 120
            + G+ +T  PP++R +AMVFQSYALYPH++V ENM+ AL+  +     I  +V  A+  
Sbjct: 61  ILDGRDITEVPPSQRDLAMVFQSYALYPHMTVEENMSFALRLAKVDPAIIQEKVKMAADK 120

Query: 121 LSLEDYLDRRPSELSGGQRQRVAIGRAVVREPKLFLFDEPLSNLDAALRMNTRLEIARLH 180
           L+L  YL R P  LSGGQRQRVAIGR++VR PK+FLFDEPLSNLDAALR NTR+EIA LH
Sbjct: 121 LNLTAYLQRTPKALSGGQRQRVAIGRSIVRSPKVFLFDEPLSNLDAALRGNTRVEIASLH 180

Query: 181 RQLSASMIYVTHDQIEAMTLADKIVVLRDGRIEQVGTPMELYNNPANRFVAEFIGAPAMN 240
           R+L A+ +YVTHDQ+EAMTLAD++VVLRDG IEQVGTP+ELY+ P NRFVA FIG P MN
Sbjct: 181 RELGATTVYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDQPINRFVARFIGMPQMN 240

Query: 241 FVPAQRLGGNPGQF--IGIRPEYAR-ISPV-GPLAGEVIHVEKLGGDTNILVDMGE---D 293
             PA   G  P Q   +GIRPE+ + +SP  G LAG+V+ VE LG +T + V   +   +
Sbjct: 241 VAPASLFGQFPAQVAEVGIRPEHLQMVSPEDGLLAGKVVLVEALGNETLVHVRPDKVQLE 300

Query: 294 LTFTARLFGQHDTNVGETLQFDFDPANCLS-FDEAGQRI 331
                RL+G+   +VG+ +   +D +  +  FD  G R+
Sbjct: 301 EPLIVRLYGRTTVHVGDRVGLKWDDSKHIHYFDTKGMRL 339


Lambda     K      H
   0.320    0.137    0.391 

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: 373
Number of extensions: 17
Number of successful extensions: 1
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: 331
Length of database: 348
Length adjustment: 28
Effective length of query: 303
Effective length of database: 320
Effective search space:    96960
Effective search space used:    96960
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 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