GapMind for catabolism of small carbon sources

 

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

Align β-Glucoside (salicin, arbutin, cellobiose, etc) group translocator, BglF (characterized)
to candidate WP_034281422.1 BA81_RS07770 PTS transporter subunit EIIC

Query= TCDB::P08722
         (625 letters)



>NCBI__GCF_000691165.1:WP_034281422.1
          Length = 619

 Score =  334 bits (856), Expect = 8e-96
 Identities = 208/612 (33%), Positives = 316/612 (51%), Gaps = 30/612 (4%)

Query: 2   TELARKIVAGVGGADNIVSLMHCATRLRFKLKDESKAQAEVLKKTPGIIMVVESGGQFQV 61
           T++A+ ++  +GG +NI  L HC+TRLRF L D+ KA    L+KTPG+I  V   GQ QV
Sbjct: 4   TQVAKDVLQHIGGKENIAHLEHCSTRLRFTLIDQKKADVPALEKTPGVI-AVRMSGQCQV 62

Query: 62  VIGNHVADVFLAVNSVAGLDEKAQQAPENDDK-----GNLLNRFVYVISGIFTPLIGLMA 116
           VIGN V +V+  V S+ G    +Q  P N  K     G +L  F+    G+F PL+  +A
Sbjct: 63  VIGNDVIEVYQKVTSLIGSSSSSQDVPSNQPKEKRKAGTVLLDFIV---GVFQPLVPAIA 119

Query: 117 ATGILKGMLALALTFQWTTEQSGTYLILFSASDALFWFFPIILGYTAGKRFGGNPFTAMV 176
             GILK  L L     W   +  TY IL    DA  +F P+++  T   +   NP  A+ 
Sbjct: 120 GGGILKSFLLLFSLLGWMDAKGQTYQILNMVGDAPLYFLPLLVAVTTANKLKVNPLVALS 179

Query: 177 IGGALVHPLILTAFENGQKADALGLDFLGIPVTLLNYSSSVIPIIFSAWLCSILERRLNA 236
             GAL+ P +      G +        L   V  + Y+  V P I S  L + +E+    
Sbjct: 180 AVGALLLPNMTAMLTEGAQ-------LLSFDVKNIAYAYQVFPAILSVLLYAQMEKFFTR 232

Query: 237 WLPSAIKNFFTPLLCLMVITPVTFLLVGPLSTWISELIAAGYLWLYQAVPAFAGAVMGGF 296
           + P  I+ FF P++ L++  PVT LL+GP+     +  ++  L ++  V   A A++   
Sbjct: 233 FSPKPIRIFFVPMMSLVITVPVTLLLLGPIGFTAGQGFSSIILAMFNTVGWVAVAILAAV 292

Query: 297 WQIFVMFGLHWGLVPLCINNFTVLGYDTM-IPLLMPAIMAQVGAALGVFLCERDAQKKVV 355
               V  G+H  +VP  +     LG + + +P  +   +A+ GA   V L  +D   +  
Sbjct: 293 LPFMVASGMHKAMVPYAVTTMGTLGKEALYLPASLAHNIAESGACFAVALRTKDKVLRST 352

Query: 356 AGSAALTSLFGITEPAVYGVNLPRKYPFVIACISGALGATIIGYAQTKVYSFGLPSIFTF 415
           A SA +++ FGITEPA+YGV L  K       I   +G   IG    + +    P + + 
Sbjct: 353 AISAGISAFFGITEPALYGVTLQNKRVLGSVMIGSFVGGIFIGLVGIQAFVLVGPGLASM 412

Query: 416 MQTIPSTGIDFTVWASVIGGVIAIGCAFVGTVMLHFITAKRQPAQGAPQEKTPEVITPPE 475
              I S  +   +  ++IG VI+   AF+      F+  K +  +    EKT +     E
Sbjct: 413 SMFI-SDELPRNLMFAIIGAVISFIVAFIAA----FVLGKDRTVE----EKTKDQAAFAE 463

Query: 476 QGG----ICSPMTGEIVPLIHVADTTFASGLLGKGIAILPSVGEVRSPVAGRIASLFATL 531
           Q G      SP+ G+++ L  V D  F+S ++G GIAI+PS G + +PV G +  LF T 
Sbjct: 464 QIGAGETFKSPVIGQMISLSEVKDDIFSSKVMGDGIAIVPSKGALYAPVDGEVTLLFETN 523

Query: 532 HAIGIESDDGVEILIHVGIDTVKLDGKFFSAHVNVGDKVNTGDRLISFDIPAIREAGFDL 591
           HA+G+++D GVE+L H+GIDTV+L+G++F   V  GD+V  GD LI FD+  I EAG+D 
Sbjct: 524 HALGMKTDQGVEVLFHIGIDTVQLEGQYFYPKVQAGDRVQAGDLLIEFDLEKIMEAGYDP 583

Query: 592 TTPVLISNSDDF 603
            T  +I+N+D +
Sbjct: 584 VTLAVITNTDQY 595


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: 1001
Number of extensions: 60
Number of successful extensions: 7
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: 619
Length adjustment: 37
Effective length of query: 588
Effective length of database: 582
Effective search space:   342216
Effective search space used:   342216
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