GapMind for catabolism of small carbon sources

 

Alignments for a candidate for MFS-glucose in Pantoea rwandensis LMG 26275

Align Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized)
to candidate WP_084932255.1 HA51_RS04135 sugar porter family MFS transporter

Query= TCDB::Q8NTX0
         (491 letters)



>NCBI__GCF_002095475.1:WP_084932255.1
          Length = 474

 Score =  432 bits (1112), Expect = e-126
 Identities = 224/452 (49%), Positives = 308/452 (68%), Gaps = 4/452 (0%)

Query: 22  EGPYRKRLFYVALVATFGGLLFGYDTGVINGALNPMTRELGLTAFTEGVVTSSLLFGAAA 81
           +  +++ +  + ++ATFGGLLFGYD GVINGAL  M + LGL + + G++TS+LL GA  
Sbjct: 4   QAEHKRYMRKIIVIATFGGLLFGYDVGVINGALPYMAKSLGLNSLSTGLITSALLMGAVF 63

Query: 82  GAMFFGRISDNWGRRKTIISLAVAFFVGTMICVFAPSFAVMVVGRVLLGLAVGGASTVVP 141
           GA+  G++SD  GRRK I+ LA+ FFV T+ C  AP    M+V R +LG AVGGAS  VP
Sbjct: 64  GAILGGKLSDLVGRRKNILFLALLFFVSTLGCSIAPDIQTMMVCRFVLGFAVGGASVTVP 123

Query: 142 VYLAELAPFEIRGSLAGRNELMIVVGQLAAFVINAIIGNVFGHHDGVWRYMLAIAAIPAI 201
            YLAE+AP + RG +   NELMIV G L AF+ NA++G   G ++ VWRYMLA+A IPA+
Sbjct: 124 TYLAEMAPAQSRGRMVTWNELMIVGGVLIAFISNAVLGITLGENEHVWRYMLALAMIPAV 183

Query: 202 ALFFGMLRVPESPRWLVERGRIDEARAVLETIRPLERAHAEVADVEHLAREEHAVSEKSM 261
            LFFGML VPESPRWLV++GR  EA++VLE IR    A  E+ +++H    E  + +  +
Sbjct: 184 CLFFGMLTVPESPRWLVKQGREAEAKSVLERIRDEHTAGIELYNIKHAISHEQQLGK--V 241

Query: 262 GLREILSSKWLVRILLVGIGLGVAQQLTGINSIMYYGQVVLIEAGFSENAALIANVAPGV 321
             RE L+  W+ RI+L+GI + V  Q TG+NSIMY+G  +L +AG   +AALI N A G+
Sbjct: 242 KFRE-LNIPWIRRIMLIGIAVAVFSQTTGVNSIMYFGTEILRDAGLETSAALIGNTAFGL 300

Query: 322 IAVVGAFIALWMMDRINRRTTLITGYSLTTISHVLIGIASVAFPVGDPLRPYVILTLVVV 381
           I+V+  F  +W++DR  RR  ++ G + TT+  ++I IA+ +   G+P  PYV+LTL V+
Sbjct: 301 ISVLSTFAGIWLLDRAGRRPMMLVGLAGTTVILLVIAIAT-SMLAGNPAMPYVVLTLTVI 359

Query: 382 FVGSMQTFLNVATWVMLSELFPLAMRGFAIGISVFFLWIANAFLGLFFPTIMEAVGLTGT 441
           F+  MQ  +    WV LSE+FPL +RG  +GISV FLWI N F+GL FP ++E  GL+GT
Sbjct: 360 FLAFMQGAIGPVLWVTLSEIFPLRIRGAGMGISVAFLWITNFFIGLTFPMMLEGFGLSGT 419

Query: 442 FFMFAGIGVVALIFIYTQVPETRGRTLEEIDE 473
           FF FA IGVV  I +    PET+G++LEEI+E
Sbjct: 420 FFAFAAIGVVGFIIMKMFFPETKGKSLEEIEE 451


Lambda     K      H
   0.327    0.142    0.420 

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: 639
Number of extensions: 35
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: 491
Length of database: 474
Length adjustment: 34
Effective length of query: 457
Effective length of database: 440
Effective search space:   201080
Effective search space used:   201080
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: 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