GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PLT5 in Bacteroides clarus YIT 12056

Align polyol transporter 5 (characterized)
to candidate WP_009122015.1 BUB52_RS10060 sugar porter family MFS transporter

Query= CharProtDB::CH_091483
         (539 letters)



>NCBI__GCF_900129655.1:WP_009122015.1
          Length = 479

 Score =  262 bits (670), Expect = 2e-74
 Identities = 154/475 (32%), Positives = 260/475 (54%), Gaps = 36/475 (7%)

Query: 37  FACAILASMTSILLGYDIGVMSGAMIYIKRDLKINDLQIGILAGSLNIYSLIGSCAAGRT 96
           +  AI+A+   +L G+D GV+SGA+ ++++D  I+D  I ++  +  + ++ G+   G+ 
Sbjct: 14  YVIAIIAATGGLLFGFDTGVISGAIPFLQKDFGIDDGVIELITTAGLVGAIAGALFCGKV 73

Query: 97  SDWIGRRYTIVLAGAIFFAGAILMGLSPNYAFLMFGRFIAGIGVGYALMIAPVYTAEVSP 156
           +D++GR+  I+ +  IF  GA+  G++P+   L+  R   GI +G +    P+Y AE+SP
Sbjct: 74  TDYLGRKKVILASAVIFAIGAVWSGIAPDSTNLILARLFLGIAIGVSSFAVPLYIAEISP 133

Query: 157 ASSRGFLNSFPEVFINAGIMLGYVSNLAFSNLPLKVGWRLMLGIGAVPSVILAIGVLAMP 216
            + RG L S  ++ +  G+++ Y+S+L F++      WR M   G +P++IL IG+  MP
Sbjct: 134 TNIRGTLVSMFQLMVTLGVLVSYLSDLFFADEVDVTCWRPMFYAGILPALILLIGMFCMP 193

Query: 217 ESPRWLVMQGRLGDAKRVLDKTSDSPTEATLRLEDIKHAAGIPADCHDDVVQVSRRNSHG 276
           ESPRWL+ +GR   A  +L+K      E     E++ H+  I  +      ++S+     
Sbjct: 194 ESPRWLMSKGRKQKAMLILNK-----IEGHGAAEEVAHS--INEEIEKSKNEISK----- 241

Query: 277 EGVWRELLIRPTPAVRRVMIAAIGIHFFQQASGIDAVVLFSPRIFKTAGLKTDHQQLLAT 336
              W EL+    P +R  +  AIGI FFQQ  GI+ V+ +SP+IF  AG       + A 
Sbjct: 242 ---WSELI---KPTLRTPLFIAIGIMFFQQFVGINTVIYYSPKIFFMAGFDGAVSAIWAA 295

Query: 337 VAVGVVKTSFILVATFLLDRIGRRPLLLTSVGGMVLSLAALGTSLTIIDQSEKKVMWAVV 396
           V VGVV     LV+ + +DR+GRR L  T + G++LSL  L  S   +++      W  V
Sbjct: 296 VGVGVVNVVATLVSIYFVDRLGRRKLYFTGLTGIILSLITLSLSFVFVNELGNAGQWLTV 355

Query: 397 VAIATVMTYVATFSIGAGPITWVYSSEIFPLRLRSQGSSMGVVVNRVTSGVISISFLPMS 456
           +    +  YVA F+I  GP+ W+  SE+FP ++R  G+S+G +   V + ++S +F  + 
Sbjct: 356 I---FMFLYVAFFAISIGPLGWLIISEVFPQKVRGLGASVGSLSVWVFNSIVSFTFFKIV 412

Query: 457 KAMT---------------TGGAFYLFGGIATVAWVFFYTFLPETQGRMLEDMDE 496
            A+T                 GAF  +G IA +A ++ Y ++PET+G  LE +++
Sbjct: 413 NALTIPGTEIMVDGEQVGNPAGAFGFYGLIALLALIWGYFYVPETKGISLEKIED 467


Lambda     K      H
   0.322    0.137    0.410 

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: 746
Number of extensions: 43
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: 539
Length of database: 479
Length adjustment: 34
Effective length of query: 505
Effective length of database: 445
Effective search space:   224725
Effective search space used:   224725
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 (21.9 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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