GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_17605 in Sinorhizobium meliloti 1021

Align ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale)
to candidate SMc02121 SMc02121 general L-amino acid transport ATP-binding ABC transporter protein

Query= uniprot:A0A1N7U8S3
         (276 letters)



>FitnessBrowser__Smeli:SMc02121
          Length = 258

 Score =  227 bits (578), Expect = 2e-64
 Identities = 123/255 (48%), Positives = 171/255 (67%), Gaps = 12/255 (4%)

Query: 22  TAAIKLQVEGIHKRYGEHEVLKGVSLNARQGDVISLIGASGSGKSTMLRCINFLEQPDAG 81
           T  + +++  ++K YG+  VL+ ++L   +G+ I + G SGSGKSTM+RCIN LE+   G
Sbjct: 14  TTDVAIEITNMNKWYGDFHVLRDINLRVMRGERIVVAGPSGSGKSTMIRCINRLEEHQKG 73

Query: 82  VITLDGISIEMRQGRAGTRAPHQDQLQNLRTRLAMVFQHFNLWSHMTVLENITMAPRRVL 141
            I +DGI +               ++  +R  + MVFQHFNL+ H+T+LEN T+AP  V 
Sbjct: 74  KIVVDGIEL----------TNDLKKIDEVRREVGMVFQHFNLFPHLTILENCTLAPIWVR 123

Query: 142 DVSAAEAEKRARMYLDKVGLPSRVADQYPAFLSGGQQQRVAIARALAMEPEIILFDEPTS 201
            +   EAE+ A  +L++V +P + A +YP  LSGGQQQRVAIAR+L M P+I+LFDEPTS
Sbjct: 124 KMPKKEAEQVAMHFLERVKIPEQ-ALKYPGQLSGGQQQRVAIARSLCMRPKILLFDEPTS 182

Query: 202 ALDPELVGEVLKVIQTLAEEGRTMLMVTHEMGFARQVSSQVLFLHQGR-VEEHGDARILD 260
           ALDPE+V EVL  +  LAEEG TM+ VTHEMGFARQV+++V+F+ QG+ VE++  A   D
Sbjct: 183 ALDPEMVKEVLDTMVGLAEEGMTMICVTHEMGFARQVANRVIFMDQGQIVEQNSPAEFFD 242

Query: 261 QPNSERLQQFLSNRL 275
            P  ER + FLS  L
Sbjct: 243 NPQHERTKLFLSQIL 257


Lambda     K      H
   0.319    0.133    0.372 

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: 203
Number of extensions: 8
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: 276
Length of database: 258
Length adjustment: 25
Effective length of query: 251
Effective length of database: 233
Effective search space:    58483
Effective search space used:    58483
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: 47 (22.7 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