GapMind for catabolism of small carbon sources

 

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

Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate 7026050 Shewana3_3192 sulfate ABC transporter, ATPase subunit (RefSeq)

Query= CharProtDB::CH_024626
         (378 letters)



>FitnessBrowser__ANA3:7026050
          Length = 376

 Score =  240 bits (612), Expect = 5e-68
 Identities = 128/244 (52%), Positives = 166/244 (68%), Gaps = 4/244 (1%)

Query: 18  VQLAGIRKCFDGKEVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIMLD 77
           ++L  I K F   + +  L+L I  GE + LLGPSG GKTT+LR+IAGLE  DSG+I   
Sbjct: 3   IRLTNISKKFGQFQALSPLNLDIQEGEMIGLLGPSGSGKTTLLRIIAGLEGADSGQIHFG 62

Query: 78  NEDITHVPAENRYVNTVFQSYALFPHMTVFENVAFGLRM----QKTPAAEITPRVMEALR 133
           N D+T V   +R V  VFQ+YALF HMTV +NVAFGL +    Q+   AEI  RV   L 
Sbjct: 63  NRDVTQVHVRDRRVGFVFQNYALFRHMTVADNVAFGLEVIPKKQRPSKAEIQKRVSHLLE 122

Query: 134 MVQLETFAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKAL 193
           MVQL   AQR P QLSGGQ+QR+A+ARA+  +P +LLLDE   ALD K+RK+++  L++L
Sbjct: 123 MVQLGHLAQRYPEQLSGGQKQRIALARALATQPEVLLLDEPFGALDAKVRKELRRWLRSL 182

Query: 194 QRKLGITFVFVTHDQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGEINM 253
             +L  T VFVTHDQ+EAL +SDR+VVM +G IEQ  TP E+Y +P + FV  F+G +N 
Sbjct: 183 HDELKFTSVFVTHDQDEALELSDRVVVMSNGNIEQVNTPIELYAQPNSRFVFDFLGNVNR 242

Query: 254 FNAT 257
           F A+
Sbjct: 243 FEAS 246


Lambda     K      H
   0.319    0.136    0.385 

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: 348
Number of extensions: 13
Number of successful extensions: 2
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: 378
Length of database: 376
Length adjustment: 30
Effective length of query: 348
Effective length of database: 346
Effective search space:   120408
Effective search space used:   120408
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 (21.7 bits)
S2: 50 (23.9 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