GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapP in Shewanella oneidensis MR-1

Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized)
to candidate 203725 SO4655 sulfate ABC transporter, ATP-binding protein (NCBI ptt file)

Query= reanno::Smeli:SMc02121
         (258 letters)



>FitnessBrowser__MR1:203725
          Length = 354

 Score =  158 bits (400), Expect = 1e-43
 Identities = 92/245 (37%), Positives = 148/245 (60%), Gaps = 10/245 (4%)

Query: 17  VAIEITNMNKWYGDFHVLRDINLRVMRGERIVVAGPSGSGKSTMIRCINRLEEHQKGKIV 76
           ++I I  +NK +G+F  +  +NL +  GE   + GPSGSGK+T++R I  LE+   G + 
Sbjct: 1   MSIHIQQVNKHFGNFVAVDSVNLEIKTGELTALLGPSGSGKTTLLRIIAGLEQADSGIVK 60

Query: 77  VDGIELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENC----TLAPIWVRKMPKKEAEQ 132
            +G ++T   + + E  R VG VFQH+ LF H+T+ EN     T+ P   R    + AE+
Sbjct: 61  FNGEDITT--QHVSE--RGVGFVFQHYALFKHMTVFENVAYGLTVRPRKTRPSKAEIAEK 116

Query: 133 VAMHFLERVKIPEQALKYPGQLSGGQQQRVAIARSLCMRPKILLFDEPTSALDPEMVKEV 192
           V    L+ V++   A +YP QLSGGQ+QR+A+AR+L + PK+LL DEP  ALD ++  E+
Sbjct: 117 VHS-LLKLVQLDWTADRYPSQLSGGQRQRIALARALAVEPKVLLLDEPFGALDAKVRAEL 175

Query: 193 LDTMVGLAEE-GMTMICVTHEMGFARQVANRVIFMDQGQIVEQNSPAEFFDNPQHERTKL 251
              +  L +E  +T + VTH+   A +VA++++ M++G+I +Q +P E +D P +     
Sbjct: 176 RRWLRRLHDEINVTTVFVTHDQEEALEVADKIVVMNKGRIEQQGTPEEVYDTPSNPFVYE 235

Query: 252 FLSQI 256
           FL  +
Sbjct: 236 FLGNV 240


Lambda     K      H
   0.322    0.136    0.397 

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: 211
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: 258
Length of database: 354
Length adjustment: 27
Effective length of query: 231
Effective length of database: 327
Effective search space:    75537
Effective search space used:    75537
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 (21.9 bits)
S2: 48 (23.1 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