GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bztD in Shewanella sp. ANA-3

Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate 7026050 Shewana3_3192 sulfate ABC transporter, ATPase subunit (RefSeq)

Query= TCDB::Q52666
         (263 letters)



>lcl|FitnessBrowser__ANA3:7026050 Shewana3_3192 sulfate ABC
           transporter, ATPase subunit (RefSeq)
          Length = 376

 Score =  153 bits (386), Expect = 6e-42
 Identities = 87/247 (35%), Positives = 145/247 (58%), Gaps = 14/247 (5%)

Query: 21  IAIQISQMNKWYGQFHVLRDINLTVHRGERIVIAGPSGSGKSTMIRCINRLEEHQSGKII 80
           ++I+++ ++K +GQF  L  +NL +  GE I + GPSGSGK+T++R I  LE   SG+I 
Sbjct: 1   MSIRLTNISKKFGQFQALSPLNLDIQEGEMIGLLGPSGSGKTTLLRIIAGLEGADSGQIH 60

Query: 81  VDGIELTSDLKNIDKVRSEVGMVFQHFNLFPHLTILENLTLAPIWVRKVPKR------EA 134
               ++T     +      VG VFQ++ LF H+T+ +N+      +  +PK+      E 
Sbjct: 61  FGNRDVTQ----VHVRDRRVGFVFQNYALFRHMTVADNVAFG---LEVIPKKQRPSKAEI 113

Query: 135 EETAMYYLEKVKIPEQAQKYPGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSALDPEMIK 194
           ++   + LE V++   AQ+YP QLSGGQ+QR+A+AR+L  +P+++L DEP  ALD ++ K
Sbjct: 114 QKRVSHLLEMVQLGHLAQRYPEQLSGGQKQRIALARALATQPEVLLLDEPFGALDAKVRK 173

Query: 195 EVLDTMIQLAEE-GMTMLCVTHEMGFAQAVANRVIFMADGQIVEQNNPHDFFHNPQSERT 253
           E+   +  L +E   T + VTH+   A  +++RV+ M++G I + N P + +  P S   
Sbjct: 174 ELRRWLRSLHDELKFTSVFVTHDQDEALELSDRVVVMSNGNIEQVNTPIELYAQPNSRFV 233

Query: 254 KQFLSQI 260
             FL  +
Sbjct: 234 FDFLGNV 240


Lambda     K      H
   0.320    0.134    0.391 

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: 232
Number of extensions: 11
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: 263
Length of database: 376
Length adjustment: 27
Effective length of query: 236
Effective length of database: 349
Effective search space:    82364
Effective search space used:    82364
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: 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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