GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SOT in Psychromonas ossibalaenae JAMM 0738

Align polyol transporter 5 (characterized)
to candidate WP_019614605.1 G327_RS0109855 sugar porter family MFS transporter

Query= CharProtDB::CH_091483
         (539 letters)



>NCBI__GCF_000381745.1:WP_019614605.1
          Length = 466

 Score =  224 bits (571), Expect = 5e-63
 Identities = 146/481 (30%), Positives = 244/481 (50%), Gaps = 44/481 (9%)

Query: 31  KRNNYAFACAILASMTSILLGYDIGVMSGAMIYIKRDLKINDLQIGILAGSLNIYSLIGS 90
           K N       I+ ++  +L GYD  V+SGA   +     ++  ++G  A S  +   IG+
Sbjct: 2   KDNINVLHVTIVVALGGLLFGYDTAVISGATGSLTHFFGLSATELGFAASSALVGCFIGA 61

Query: 91  CAAGRTSDWIGRRYTIVLAGAIFFAGAILMGLSPNYAFLMFGRFIAGIGVGYALMIAPVY 150
             AG+ SD +GRR  + +A  +F   AI   +  NY   +F R + GIGVG A M++P+Y
Sbjct: 62  LVAGKISDSMGRRGALKIAATLFLISAIGTAVPDNYWVFVFFRIVGGIGVGIASMVSPMY 121

Query: 151 TAEVSPASSRGFLNSFPEVFINAGIMLGYVSN----LAFSNLPLK-VGWRLMLGIGAVPS 205
            AEV+P + RG L S  +  I  G+++ Y  N    LA + + L  VGWR M     +P+
Sbjct: 122 IAEVAPPNKRGALVSCNQFAIIFGMLVVYFVNYGIALAGTEVWLNTVGWRYMFASECIPA 181

Query: 206 VILAIGVLAMPESPRWLVMQGRLGDAKRVLDKTSDSPTEATLRLEDIKHA-AGIPADCHD 264
           ++  + +  +PE+PRWL ++GR  +A+ +L         A  + EDI+    GI +   D
Sbjct: 182 LLFLVLLFTVPETPRWLALKGRNQEARNLL--------RALNKNEDIEEQWQGIQSSLGD 233

Query: 265 DVVQVSRRNSHGEGVWRELLIRPTPAVRRVMIAAIGIHFFQQASGIDAVVLFSPRIFKTA 324
              +VS                    +  V++  I +   QQ +GI+  + ++P IFK+ 
Sbjct: 234 TKGKVS---------------IAALGMMGVLVIGIMLSVLQQVTGINVFLYYAPEIFKSF 278

Query: 325 GLKTDHQQLLATVAVGVVKTSFILVATFLLDRIGRRPLLLTSVGGMVLSLAALGTSLTII 384
              +    LL T+ +G V  +F  +A F +D+ GRRPL++   G M +S+ A+GT+    
Sbjct: 279 SDSSTDTALLQTILIGAVNLTFTAIAIFTVDKFGRRPLMIIGAGAMAVSMIAIGTA---- 334

Query: 385 DQSEKKVMWAVVVAIATVMTYVATFSIGAGPITWVYSSEIFPLRLRSQGSSMGVVVNRVT 444
             +    +   ++    V+ Y+A F++  GP+TWV  SEIFP  +RS+  S+ V      
Sbjct: 335 --AYSNAIGGYLLFF--VLLYIAAFALSLGPVTWVLLSEIFPNSIRSKALSIAVFAQWFA 390

Query: 445 SGVISISFLPMS-------KAMTTGGAFYLFGGIATVAWVFFYTFLPETQGRMLEDMDEL 497
           + V+S SF  M+       +    G  F+L+G        F + F+PET+G+ LED++++
Sbjct: 391 NFVVSQSFPMMNDSNGYLFQTYNGGFPFWLYGFFGVFTVYFIWKFVPETKGKSLEDLEKI 450

Query: 498 F 498
           +
Sbjct: 451 W 451


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: 696
Number of extensions: 41
Number of successful extensions: 5
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: 466
Length adjustment: 34
Effective length of query: 505
Effective length of database: 432
Effective search space:   218160
Effective search space used:   218160
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