GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc04256 in Magnetospirillum magneticum AMB-1

Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate WP_011385004.1 AMB_RS13205 polyamine ABC transporter ATP-binding protein

Query= reanno::Smeli:SMc04256
         (361 letters)



>NCBI__GCF_000009985.1:WP_011385004.1
          Length = 379

 Score =  206 bits (523), Expect = 1e-57
 Identities = 118/287 (41%), Positives = 172/287 (59%), Gaps = 5/287 (1%)

Query: 9   LSLNFGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFIKDRNVT 68
           +S  FG  T ++ ++L I  GEF  LLG+SGCGK+TLL  +AG    + G+I I  ++VT
Sbjct: 28  ISKRFGDFTAVEHVDLAIHKGEFFSLLGASGCGKTTLLRMLAGFEIPTTGRILIDGQDVT 87

Query: 69  WEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQIQPLLK 128
              P +R + M+FQSYAL+P M+V  N++FGLK   +    I+ +V  A E++Q+     
Sbjct: 88  EVPPYERPVNMMFQSYALFPHMSVADNIAFGLKQDGLAKPVIKDKVAAALELVQMGRFSG 147

Query: 129 RKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQSLKNTMI 188
           RKP +LSGGQRQRVA+ R L ++  V L DEPL+ LD KLR   ++E+  +   +  T +
Sbjct: 148 RKPHQLSGGQRQRVALARCLAKEPKVVLLDEPLAALDKKLREATQLELVNIQDRVGITFV 207

Query: 189 YVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMNFFRGEVEP 248
            VTHDQ EA+T++ RI VM +G I+Q+  P+ IY  P   FVA FIG  + N F+G V  
Sbjct: 208 MVTHDQGEAMTMSSRIGVMNAGCIEQVGSPVDIYEYPGTRFVADFIG--AANMFQGSVRG 265

Query: 249 KDGRSFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEARD 295
            +G   +    +  D++   A   +  G  V + +RPE V +  ARD
Sbjct: 266 GEGALAIACPELEHDLSVTEAGA-VAAGTPVTVMVRPEKVMI--ARD 309


Lambda     K      H
   0.320    0.137    0.392 

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: 341
Number of extensions: 15
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: 361
Length of database: 379
Length adjustment: 30
Effective length of query: 331
Effective length of database: 349
Effective search space:   115519
Effective search space used:   115519
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 Sep 17 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