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_089137055.1 CES79_RS09755 ABC transporter substrate-binding protein/permease

Query= TCDB::Q8YSA2
         (501 letters)



>NCBI__GCF_002217945.1:WP_089137055.1
          Length = 496

 Score =  228 bits (582), Expect = 3e-64
 Identities = 154/469 (32%), Positives = 250/469 (53%), Gaps = 40/469 (8%)

Query: 29  QGKTLRIATEPAFPPFEF-TAQGGNLQ--GFSIDLMNAIASAANLKVNFQSLPFDGIIPA 85
           +GK + +AT P +PP+EF  ++ G  Q  G  +D+M  +A    +K+  +S+ F  ++ A
Sbjct: 49  RGKII-MATSPDYPPYEFQVSKHGKSQVVGMDVDIMKQVAKDLGVKLVVKSMSFSNVLVA 107

Query: 86  LQSRTVDAAISSITITAERAETVAFSRPYFKAGLAIAIRSSNED-ITGFDSLKNKKIAVQ 144
           +++   D A+S I  T ER ++V FS+ Y+  G +  I  ++    T   SL +K I  Q
Sbjct: 108 VETGKADVAMSGINPTPERRQSVDFSKIYYNGGQSFLINKTDAGKYTNKASLAHKIIGAQ 167

Query: 145 IGTTGAGKAKS-IPGAQIRSFDSAPLALQELLNNNVDAVINDAP-VTLYAINTGNLQGIK 202
            GT     AKS IPGA+++  D     +  L  + +DA+  + P    Y  N  +L+ IK
Sbjct: 168 TGTLQYNLAKSKIPGAKVKGMDKNTDLVLALKTHKIDALGIETPSAEAYVKNDPDLKMIK 227

Query: 203 VVEKLLTEEYYGIATAQ---NSPYLALINDGLNRVLADGSYSQIYQ---KWFKVEPPSLP 256
               L   +  G A A    +   +A IN  + ++ A G  +Q      K+ KV      
Sbjct: 228 SGYNLNKNDT-GSAMALKKGSGTLVAAINKSITKIKAKGLPNQYLAQAGKYMKV------ 280

Query: 257 DKSLYENQTNTHKSGSINLILQFLPTLLQGALVTIQLTILSTVLGLICGTLIALTRLSQF 316
                    NTH +  ++    F     +G   T+ ++ +S + G++ GT++AL R S+ 
Sbjct: 281 ---------NTHNTSMMHYWTYFA----KGIEYTLIISAISVIFGVLLGTILALMRFSKS 327

Query: 317 TPARLFARAYVDFFRGTPLLVQIFMIYFGIPALAQQLGFTFNFDRWVAGVIALSVNAAAY 376
                 + AYV+F RGTPL+VQ+  +YFGI       G   N    ++G+IA+S+N+ AY
Sbjct: 328 KLLHAISIAYVEFVRGTPLMVQVMFVYFGI-------GIVVNLPALLSGIIAVSLNSGAY 380

Query: 377 IAEIVRAGIQSIETGQTEAAKSLGLNPWLTMRLVIFPQAFRRMLPPLGNEFISLLKDTSL 436
           + EI+R GI S++ GQTEA+ SLGL    TMR V+ PQA + + P LGNEF+SL+K++S+
Sbjct: 381 VEEIIRGGINSVDKGQTEASASLGLAKTDTMRFVVLPQALKNIWPALGNEFVSLIKESSI 440

Query: 437 VAVIGFEELFRKGQLIVADNYRAFEIYAAVAIVYLCLTLLASQVLSRLE 485
           V++IG  +L  +  ++ AD YR         I+Y  +T + ++VL+  E
Sbjct: 441 VSIIGVTDLIYQLNIVRADTYRGVMPVFVAMIIYFVMTFILTRVLNYFE 489


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: 477
Number of extensions: 20
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: 501
Length of database: 496
Length adjustment: 34
Effective length of query: 467
Effective length of database: 462
Effective search space:   215754
Effective search space used:   215754
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