GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtB in Lactobacillus silagei IWT126

Align Basic amino acid uptake transporter, BgtAB (characterized)
to candidate WP_089136315.1 CES79_RS03445 ABC transporter permease subunit

Query= TCDB::Q8YSA2
         (501 letters)



>NCBI__GCF_002217945.1:WP_089136315.1
          Length = 479

 Score =  244 bits (624), Expect = 4e-69
 Identities = 165/486 (33%), Positives = 254/486 (52%), Gaps = 35/486 (7%)

Query: 15  LICLFLT-GCSGNLSQGKTL-RIATEPAFPPFEFTAQGGNLQGFSIDLMNAIASAANLKV 72
           LI +F+T G     ++  T  ++AT+  FPPFEF        G  IDL++AIA     KV
Sbjct: 15  LIAMFITFGLGATPAKATTTYQVATDSTFPPFEFANSHNKYVGIDIDLLHAIAKDQGFKV 74

Query: 73  NFQSLPFDGIIPALQSRTVDAAISSITITAERAETVAFSRPYFKAGLAIAIRSSNEDITG 132
           N +   F+  + ++QS   D  I+ ++IT ER  T  FS+PYF +G+ +A +  N  IT 
Sbjct: 75  NIKPTSFNSAVQSVQSGQADGVIAGMSITKEREATFDFSKPYFMSGVVMAAKP-NGKITK 133

Query: 133 FDSLKNKKIAVQIGTTGAGKAKSIP---GAQIRSFDSAPLALQELLNNNVDAVINDAPVT 189
              L+ K++AV+ GT+GA  A+SI    G +I +FD +    Q++L  N  A   D+PV 
Sbjct: 134 LSQLRGKRVAVKTGTSGAQYAQSIHKKYGFRIVTFDESNDMYQDVLTGNSAACFEDSPVM 193

Query: 190 LYAINTGNLQGIKVVEKLLTEEYYGIATAQ--NSPYLALINDGLNRVLADGSYSQIYQKW 247
            YA+  G    +K+  K      YG A  +  N   L + N+GL  + ++G Y++I + +
Sbjct: 194 KYAVRQGTK--LKIYTKPTLNGPYGFAVKKGHNKKLLRMFNNGLADLKSNGEYARITRHY 251

Query: 248 FKVEPPSLPDKSLYENQTNTHKSGSINLILQFLPTLLQGALVTIQLTILSTVLGLICGTL 307
              +  S            T     + L+ Q    LL G   T+ LT+++     + G +
Sbjct: 252 LGAKGSS----------DTTSDRTFLGLLKQNKGALLNGFEQTVWLTVVAIFFATLFGVI 301

Query: 308 IALTRLSQFTPARLF---ARAYVDFFRGTPLLVQIFMIYFGIPALAQQLGFTFNFDRWVA 364
           + L  +    P + F   +   +  FRG PLLV    IY GIP+L            +VA
Sbjct: 302 VGLLGV---VPNKFFNGLSTTLIYIFRGLPLLVLALFIYTGIPSLTGS-----KIPAFVA 353

Query: 365 GVIALSVNAAAYIAEIVRAGIQSIETGQTEAAKSLGLNPWLTMRLVIFPQAFRRMLPPLG 424
           G I L  N  AYIA  V+ GI +++ GQ EAA+SLGL    +MR +I PQ  R M+P   
Sbjct: 354 GTITLMFNEGAYIAAFVKGGINAVDDGQMEAARSLGLPFGKSMRRIILPQGIRIMIPSFI 413

Query: 425 NEFISLLKDTSLVAVIGFEELFRKGQLIVADNYRAFEIYAAVAIVYL----CLTLLASQV 480
           N+FI  LKDTS++++IG  EL + G++I+A N   F+++  +AI+YL     LT L++ V
Sbjct: 414 NQFIITLKDTSILSIIGIIELTQTGKIIIARNLEGFKVWTIIAIIYLIVITLLTWLSNWV 473

Query: 481 LSRLEM 486
             R+ +
Sbjct: 474 ERRIRL 479


Lambda     K      H
   0.323    0.137    0.394 

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: 562
Number of extensions: 34
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: 501
Length of database: 479
Length adjustment: 34
Effective length of query: 467
Effective length of database: 445
Effective search space:   207815
Effective search space used:   207815
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 (22.0 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