GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtB' in Azospirillum brasilense Sp245

Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate AZOBR_RS08660 AZOBR_RS08660 ABC transporter permease

Query= uniprot:Q31RP0
         (377 letters)



>FitnessBrowser__azobra:AZOBR_RS08660
          Length = 399

 Score =  271 bits (694), Expect = 2e-77
 Identities = 158/365 (43%), Positives = 230/365 (63%), Gaps = 16/365 (4%)

Query: 22  WQLLVLLVVGLGAIWLVDNLVYNLSQRGLSLSFDWLDQSAGFNIGESAIAYRTADSYARA 81
           +Q+LV+ +V     +L+ N + NLS+R ++  F +LD+ A F IGES I Y   DSY RA
Sbjct: 31  YQVLVVGIVIAVGWFLIHNTLDNLSKRSIATGFGFLDREASFGIGESLIDYHPRDSYGRA 90

Query: 82  LVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRNTPLLLQLIVW 141
            +VG++N+L+V  IG++L TV+GTL GVA  S NWL+ +L+  YV +VRN P LLQL  W
Sbjct: 91  FLVGVLNTLKVSIIGVVLATVLGTLIGVARLSSNWLIAKLASTYVEIVRNIPPLLQLFFW 150

Query: 142 YFPILLSLPAAQQPWHWLGSLYLSKQGIYLPWPQ------TPGWLVVILAIALVLFVSWL 195
           Y  +  S+P  +Q  + +  ++LS++G+++P P       T G+ + I  I ++    W 
Sbjct: 151 YALVSESMPPVRQALNPIPGVFLSQRGLFVPVPSADPVWGTMGFALAIAVIGVIFLRRWA 210

Query: 196 AQRQ-RSPRDWRWLYGAIAVVTVLMLL--------TQLSWPQQLQPGQIRGGLRLSLEFT 246
             RQ R+ + +     +++++  L L+        T L  P+ LQ     GG+ L+ EF 
Sbjct: 211 KARQERTGQPFPIGTASLSLLIGLPLIAYIAGGAPTALDVPK-LQGFNFVGGVVLTPEFF 269

Query: 247 ALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQIVVPQALRVIVPSL 306
           A+L+GLV YT AFI E++R GIL+V  GQ EAA ALG+   +TL  +V+PQALRVIVP L
Sbjct: 270 AILVGLVVYTAAFIAEVVRSGILAVNWGQTEAARALGIDSGKTLRLVVLPQALRVIVPPL 329

Query: 307 NSQYVGFAKNSSLAIAVGYPDLYATAQTTLNQTGRPVEVFLILMLTYLAINAVISAGMNG 366
            SQY+   KNSSLA+A+GYPDL + A TTLNQTG+ +E   ++M TYL I+  IS  MN 
Sbjct: 330 TSQYLNLTKNSSLALAIGYPDLVSIANTTLNQTGQAIEGVAMIMGTYLVISLGISIFMNW 389

Query: 367 LQQRL 371
             +R+
Sbjct: 390 YNKRI 394


Lambda     K      H
   0.326    0.140    0.445 

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: 406
Number of extensions: 15
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: 377
Length of database: 399
Length adjustment: 30
Effective length of query: 347
Effective length of database: 369
Effective search space:   128043
Effective search space used:   128043
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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