GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztA in Sinorhizobium meliloti 1021

Align BztA, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate SMc02118 SMc02118 general L-amino acid-binding periplasmic ABC transporter protein

Query= TCDB::Q52663
         (338 letters)



>FitnessBrowser__Smeli:SMc02118
          Length = 341

 Score =  388 bits (996), Expect = e-112
 Identities = 196/330 (59%), Positives = 237/330 (71%), Gaps = 3/330 (0%)

Query: 11  ALAALVAGAASASTLDDVKARGQLICGSNPGLTGFAAPDANGVYQGFDVAVCKAVAAAVL 70
           A+  +   AASA+TLDDVKA+G + CG N GL GFAAPDA+G + GFDV  CKA+AAA+ 
Sbjct: 13  AVVGIGTHAASAATLDDVKAKGFVQCGVNTGLAGFAAPDASGNWSGFDVDYCKAIAAAIF 72

Query: 71  GDPMKVKYVPLTGETRFTALASGEVDVLVRNSTWTFSRDTELALDFVAVNYYDGQGFMVN 130
           GD  KVKY PL+ + RF AL SGEVDVL RN+TW+ +RDT L  +F  VNYYDGQGFMV 
Sbjct: 73  GDGSKVKYTPLSAKERFPALQSGEVDVLARNTTWSINRDTALGFNFRPVNYYDGQGFMVR 132

Query: 131 KSLGVSSAKELDGATICVQTGTTTEMNLADFFKANNMTYTPVNIADDAEGQQKFAAGACD 190
           K L V SA EL GA +CVQTGTTTE+NLAD+FKANN+ Y PV      E    + AG CD
Sbjct: 133 KELDVKSALELSGAAVCVQTGTTTELNLADYFKANNLQYNPVVFEKLEEVNAAYDAGRCD 192

Query: 191 SYTTDASGLASSRATLPNAADIVILPEIISKEPLGPVVRHGDNNWGDIVRWSFYALVAAE 250
            YTTD SGL S R TL    D ++LPEIISKEPL P VR GD+ W DIV W  YALV AE
Sbjct: 193 VYTTDQSGLYSLRLTLSKPDDHIVLPEIISKEPLAPAVRQGDDQWFDIVSWVHYALVQAE 252

Query: 251 EYGITKANLEEVAASTQNPEIRRLLGLEGD--MGKKIGLDNDFAKRAILASGNYGEVFEA 308
           E+G+T+ANLEE+  ST NP+++R LG+E D  +G  +GL N++A   + A GNYGEVF+ 
Sbjct: 253 EFGVTQANLEEMKKST-NPDVQRFLGVEADSKIGTDLGLTNEWAVNIVKAVGNYGEVFDR 311

Query: 309 NIGASTSIGLARGLNAQWTQGGLMYAPPFR 338
           NIGA + + + RGLNA W +GGL YAPP R
Sbjct: 312 NIGAGSPLKIERGLNALWNKGGLQYAPPVR 341


Lambda     K      H
   0.316    0.132    0.384 

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: 381
Number of extensions: 14
Number of successful extensions: 3
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: 338
Length of database: 341
Length adjustment: 28
Effective length of query: 310
Effective length of database: 313
Effective search space:    97030
Effective search space used:    97030
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 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