GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapP in Shewanella sp. ANA-3

Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized)
to candidate 7026050 Shewana3_3192 sulfate ABC transporter, ATPase subunit (RefSeq)

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



>FitnessBrowser__ANA3:7026050
          Length = 376

 Score =  155 bits (393), Expect = 9e-43
 Identities = 91/244 (37%), Positives = 142/244 (58%), Gaps = 8/244 (3%)

Query: 17  VAIEITNMNKWYGDFHVLRDINLRVMRGERIVVAGPSGSGKSTMIRCINRLEEHQKGKIV 76
           ++I +TN++K +G F  L  +NL +  GE I + GPSGSGK+T++R I  LE    G+I 
Sbjct: 1   MSIRLTNISKKFGQFQALSPLNLDIQEGEMIGLLGPSGSGKTTLLRIIAGLEGADSGQIH 60

Query: 77  VDGIELTNDLKKIDEVRREVGMVFQHFNLFPHLTILENCT--LAPIWVRKMPKK-EAEQV 133
                   D+ ++    R VG VFQ++ LF H+T+ +N    L  I  ++ P K E ++ 
Sbjct: 61  FGN----RDVTQVHVRDRRVGFVFQNYALFRHMTVADNVAFGLEVIPKKQRPSKAEIQKR 116

Query: 134 AMHFLERVKIPEQALKYPGQLSGGQQQRVAIARSLCMRPKILLFDEPTSALDPEMVKEVL 193
             H LE V++   A +YP QLSGGQ+QR+A+AR+L  +P++LL DEP  ALD ++ KE+ 
Sbjct: 117 VSHLLEMVQLGHLAQRYPEQLSGGQKQRIALARALATQPEVLLLDEPFGALDAKVRKELR 176

Query: 194 DTMVGLAEE-GMTMICVTHEMGFARQVANRVIFMDQGQIVEQNSPAEFFDNPQHERTKLF 252
             +  L +E   T + VTH+   A ++++RV+ M  G I + N+P E +  P       F
Sbjct: 177 RWLRSLHDELKFTSVFVTHDQDEALELSDRVVVMSNGNIEQVNTPIELYAQPNSRFVFDF 236

Query: 253 LSQI 256
           L  +
Sbjct: 237 LGNV 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: 217
Number of extensions: 10
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: 376
Length adjustment: 27
Effective length of query: 231
Effective length of database: 349
Effective search space:    80619
Effective search space used:    80619
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