GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bglF in Bacillus safensis FO-36b

Align β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized)
to candidate WP_034283128.1 BA81_RS14345 PTS transporter subunit EIIC

Query= TCDB::P08722
         (625 letters)



>NCBI__GCF_000691165.1:WP_034283128.1
          Length = 618

 Score =  497 bits (1279), Expect = e-145
 Identities = 260/632 (41%), Positives = 394/632 (62%), Gaps = 28/632 (4%)

Query: 3   ELARKIVAGVGGADNIVSLMHCATRLRFKLKDESKAQAEVLKKTPGIIMVVESGGQFQVV 62
           +LA  I+  +G   N+ SL+HCATRLRF L D SKA    ++K  G++ V+ESGGQFQVV
Sbjct: 5   QLAEDIIKHIGTEKNVHSLVHCATRLRFTLNDRSKADKAAIEKLNGVVTVMESGGQFQVV 64

Query: 63  IGNHVADVFLAVNSVAGL--DEKAQQAPENDDKGNLLNRFVYVISGIFTPLIGLMAATGI 120
           IGN V +V+  +     L  D  A  A   ++  +L  +FV ++SGIFTPL+G+MA  GI
Sbjct: 65  IGNTVPEVYREIGEFTNLLEDSAASSAKSGEESTSLFGKFVDIVSGIFTPLLGVMAGAGI 124

Query: 121 LKGMLALALTFQWTTEQSGTYLILFSASDALFWFFPIILGYTAGKRFGGNPFTAMVIGGA 180
           LKG+L + +  +W + +  +Y ILF+ASD+LF+F P++L +T+ ++F  NPF A+ I GA
Sbjct: 125 LKGLLGICINAKWLSPEDTSYQILFAASDSLFYFLPLLLAFTSARKFKANPFVAVTIAGA 184

Query: 181 LVHPLILTAFENGQKADALGLDFLGIPVTLLNYSSSVIPIIFSAWLCSILERRLNAWLPS 240
           L++P I    + G       + F GIPV L++Y+S+VIPII + ++   +ER  N  +  
Sbjct: 185 LIYPTIQELSKGGGD-----VTFFGIPVVLMSYTSTVIPIILAVFVMGYIERFFNKVIHE 239

Query: 241 AIKNFFTPLLCLMVITPVTFLLVGPLSTWISELIAAGYLWLYQAVPAFAGAVMGGFWQIF 300
           ++KNF TPL+ L+ + P+T ++ GP   +    IAA  L ++   P  AGA++   WQI 
Sbjct: 240 SVKNFITPLILLVTVVPLTLIVFGPFGVYAGNGIAAVLLKVFSFSPTLAGALIAMAWQIL 299

Query: 301 VMFGLHWGLVPLCINNFTVLGYDTMIPLLMPAIMAQVGAALGVFLCERDAQKKVVAGSAA 360
           V+FG+HWGLVP+ +NN  V G D + P   PA+ +Q GA++GV L  ++ + K +AGS A
Sbjct: 300 VIFGIHWGLVPVILNNIAVHGKDHIKPATAPAVFSQAGASIGVMLKTKNKKLKSLAGSTA 359

Query: 361 LTSLFGITEPAVYGVNLPRKYPFVIACISGALGATIIGYAQTKVYSFGLPSIFTFMQTIP 420
           ++++FGITEPAVYGV L  K PF+ A IS  +G  IIGY+Q+   + GLPS+     T+P
Sbjct: 360 VSAVFGITEPAVYGVTLRLKKPFIAAVISAGVGGAIIGYSQSIAIASGLPSLL----TLP 415

Query: 421 -STGIDFTVWASVIGGVIAIGCAFVGTVMLHFITAKRQPAQGAPQEKTPEVITP------ 473
              G  FT      G +I I  +FV +++L ++   + P     +++TP    P      
Sbjct: 416 IFYGQGFT------GFIIGISVSFVLSIILTYLIGFKDPVD---EDETPAASAPVIENEH 466

Query: 474 -PEQGGICSPMTGEIVPLIHVADTTFASGLLGKGIAILPSVGEVRSPVAGRIASLFATLH 532
             +   + SP+ GE++ L  V D  F+SG LGKG AI+PS G++ +PV+G + ++F T H
Sbjct: 467 GVKAAHVKSPLKGEVIKLEEVQDKAFSSGALGKGAAIIPSEGKLFAPVSGVVTTVFPTGH 526

Query: 533 AIGIESDDGVEILIHVGIDTVKLDGKFFSAHVNVGDKVNTGDRLISFDIPAIREAGFDLT 592
           A G+ S+ G E+LIH+G+DTV+L GK F+  V  G  +  G+ L  FDI AI+ AG  +T
Sbjct: 527 AYGLTSESGAEVLIHIGLDTVQLGGKHFTPKVVQGQTITEGELLAEFDIEAIQAAGLSVT 586

Query: 593 TPVLISNSDDFTDVLPHGTAQISAGEPLLSII 624
           TPV+I+NS +F+D++     QI+ G+  L ++
Sbjct: 587 TPVIITNSGEFSDIIETEEKQITPGQSFLHLV 618


Lambda     K      H
   0.324    0.141    0.427 

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: 1181
Number of extensions: 73
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: 625
Length of database: 618
Length adjustment: 37
Effective length of query: 588
Effective length of database: 581
Effective search space:   341628
Effective search space used:   341628
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 54 (25.4 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