GapMind for catabolism of small carbon sources

 

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

Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate WP_011385763.1 AMB_RS17210 molybdenum import ATP-binding protein ModC

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



>NCBI__GCF_000009985.1:WP_011385763.1
          Length = 363

 Score =  141 bits (355), Expect = 3e-38
 Identities = 83/241 (34%), Positives = 128/241 (53%), Gaps = 32/241 (13%)

Query: 22  LDLTIEDGEF------------TVFVGPSGCGKSTLLRLIAGLEDITSGTIRIDGE---- 65
           LDL    GEF            T   G SG GK++++ ++AGL     G+I +DG     
Sbjct: 4   LDLRRRQGEFRLDVRLSAGPGVTALYGRSGSGKTSVINMVAGLSRPDEGSISVDGRVLFD 63

Query: 66  --DATNIPPAKRGLAMVFQSYALYPHMSVRKNIAFPMKMAGIPADEQKRRIDNAAAALNL 123
                ++PP  R L  VFQ + L+PH+SVR N+ F  K+  +P+ E+ + +D     L +
Sbjct: 64  SRSGIDLPPEARRLGYVFQEHRLFPHLSVRGNLEFGQKL--LPSAERTQSLDKVVELLGI 121

Query: 124 TDYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVGMRLEISELHKRL 183
              LDRRP +LSGG++QRVAIGRA++  P   L DEPL+ LD A +  +   I++L +R 
Sbjct: 122 ESLLDRRPAKLSGGEKQRVAIGRALLASPRILLMDEPLAALDPARKAEVLPFIAQLARRF 181

Query: 184 ATTMIYVTHDQVEAMTMADKIVVLQAGVIEQVGSPMELYRAPRNVFVAGFIGSPKMNLLT 243
           +  ++YV+H   E + +AD + ++  G +   G P+E             +G P +  LT
Sbjct: 182 SVPILYVSHSMDEVLRLADTLALMDGGKVAASG-PLE-----------SLMGDPGLRPLT 229

Query: 244 G 244
           G
Sbjct: 230 G 230


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: 306
Number of extensions: 19
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: 363
Length adjustment: 29
Effective length of query: 305
Effective length of database: 334
Effective search space:   101870
Effective search space used:   101870
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