GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolT in Pantoea rwandensis LMG 26275

Align Minor myo-inositol transporter, IolT2, of 478 aas (characterized)
to candidate WP_084932306.1 HA51_RS04265 sugar porter family MFS transporter

Query= TCDB::E1WAV4
         (478 letters)



>NCBI__GCF_002095475.1:WP_084932306.1
          Length = 476

 Score =  532 bits (1370), Expect = e-155
 Identities = 254/468 (54%), Positives = 348/468 (74%), Gaps = 6/468 (1%)

Query: 1   MSQRSKYNSAYVYVLCCIAALAGLMFGYSTAVITGVVLPLQQYYQLTPTETGWAVSSIVI 60
           MS + ++N+ YVY+LC  AA  G MFGYS  VI   +  +++ + L   ETGWAVSSI+ 
Sbjct: 1   MSYQHRFNARYVYMLCLAAAAGGFMFGYSEGVIAATLESIKKSFGLNSMETGWAVSSIIF 60

Query: 61  GCIIGALVGGKIADKLGRKPALLIIAIIFIASSLGAAMSESFMIFSLSRIVCGFAVGMAG 120
           G +IGAL  GK+ADK GRK  +L+ AI+F+ +S  +A+++SF +F+ +R++CG AVG+A 
Sbjct: 61  GGVIGALAAGKMADKTGRKLVMLLSAILFVITSYLSAVADSFTLFTGARLICGIAVGLAA 120

Query: 121 TASTMYMSELAPAEIRGKALGIYNISVVSGQVIVFIVNYLIAKGMPADVLVSQGWKTMLF 180
           T + MY+SE++PA++RGKA G Y++S+V+G + VF VNYLIA+GMP   +V  GW+TM+ 
Sbjct: 121 TVTPMYISEISPAKMRGKATGTYDLSIVAGVLAVFTVNYLIARGMPQAWMVETGWRTMMA 180

Query: 181 AQVVPSIAMLAITLFLPESPAWCARNNRSEARSIKVLTRIYSGLTATDVAAIFDSMKETV 240
            Q+VPS+AML + + +PESP WC R+NR E ++IKVL+RIY      +   +F       
Sbjct: 181 VQLVPSVAMLVLIILVPESPHWCIRHNRGE-QAIKVLSRIYPEFNQEEARQLFQLPSSAA 239

Query: 241 RSQDNVAGGERTNLKSSPVLRYILLVGCCIAVLQQFTGVNVMNYYAPLVLQN--SSTEVV 298
           +       G    +  +PVLRYIL+VG  IAVLQQFTG+NV+NYY P++L+   S+ +++
Sbjct: 240 KKSTTARKGV---MPENPVLRYILVVGVAIAVLQQFTGINVINYYTPMMLEGTTSNKDII 296

Query: 299 MFQTIFIAVCNVVGSFIGMILFDRYGRIPIMKIGTIGSIVGLLIASYGLYTHDTGYITIF 358
            F+TIF+A+ N VG+FIGM LFD YGR+PIMKIGT+G+I+GLLIAS+GLYT+D GYI I 
Sbjct: 297 FFETIFVALLNGVGAFIGMHLFDHYGRLPIMKIGTVGAIIGLLIASWGLYTNDVGYIAIS 356

Query: 359 GILFFMLLFAVSWSVGAWVLISEVFPEKIKGFGMGLAVSLMWIANFLISLLFPVINDNAW 418
           GIL F L F + W  GAWV+ISE+FP++I+   MGLAV LMW+ NFLI+L+FP++NDNAW
Sbjct: 357 GILIFTLFFGMGWGAGAWVMISEIFPDRIRESSMGLAVGLMWVTNFLITLVFPLVNDNAW 416

Query: 419 LQETFGGAFSMWIFVVFNLVCYVFISRYVPETKGVPLTEIERLAENKL 466
           LQE F GAFSMWIFVVFN  CY F+SRYVPET+GV L +IE++AE K+
Sbjct: 417 LQEQFHGAFSMWIFVVFNAFCYWFLSRYVPETRGVALEDIEKVAEAKM 464


Lambda     K      H
   0.327    0.140    0.419 

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: 728
Number of extensions: 23
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: 478
Length of database: 476
Length adjustment: 33
Effective length of query: 445
Effective length of database: 443
Effective search space:   197135
Effective search space used:   197135
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: 51 (24.3 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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