GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlK in Methylocystis bryophila S285

Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate WP_085769830.1 B1812_RS00440 molybdenum ABC transporter ATP-binding protein

Query= reanno::Phaeo:GFF1302
         (334 letters)



>NCBI__GCF_002117405.1:WP_085769830.1
          Length = 370

 Score =  145 bits (365), Expect = 2e-39
 Identities = 83/203 (40%), Positives = 112/203 (55%), Gaps = 14/203 (6%)

Query: 32  TVFVGPSGCGKSTLLRLIAGLEDITSGTIRIDGE-----DATNIPPAKRGLAMVFQSYAL 86
           T   GPSGCGK+T++R +AGL  +  G  RIDGE     D   +P  KR L  VFQ  +L
Sbjct: 32  TALFGPSGCGKTTVIRCVAGLTRVKDGYCRIDGEIWQDRDGVFLPTHKRPLGYVFQEASL 91

Query: 87  YPHMSVRKNIAFPMKMAGIPADEQKRR----IDNAAAALNLTDYLDRRPGQLSGGQRQRV 142
           +PH+SVR+N+ F     G P ++ K R     D     L L   L+R P  LSGG+RQRV
Sbjct: 92  FPHLSVRRNLLF-----GAPKEKSKDRPQIDFDEVVDLLGLRRLLERSPTNLSGGERQRV 146

Query: 143 AIGRAIVREPAAFLFDEPLSNLDAALRVGMRLEISELHKRLATTMIYVTHDQVEAMTMAD 202
            IGRA++ +P   L DEPLS LD   +  +   I +L    A  + Y+THD  E   +AD
Sbjct: 147 GIGRALLTQPKLLLMDEPLSALDRKTKNEILPFIEKLRDHFAVPIFYITHDITEVERLAD 206

Query: 203 KIVVLQAGVIEQVGSPMELYRAP 225
           ++V+L+ G +   G   EL   P
Sbjct: 207 QVVLLEKGHVVMAGPLAELQSNP 229


Lambda     K      H
   0.320    0.138    0.400 

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: 289
Number of extensions: 7
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: 334
Length of database: 370
Length adjustment: 29
Effective length of query: 305
Effective length of database: 341
Effective search space:   104005
Effective search space used:   104005
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