GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtB in Williamsia sterculiae CPCC 203464

Align Basic amino acid uptake transporter, BgtAB (characterized)
to candidate WP_083710231.1 BW971_RS16650 ABC transporter permease subunit

Query= TCDB::Q8YSA2
         (501 letters)



>NCBI__GCF_900156495.1:WP_083710231.1
          Length = 589

 Score =  195 bits (496), Expect = 3e-54
 Identities = 151/475 (31%), Positives = 239/475 (50%), Gaps = 47/475 (9%)

Query: 51  GNLQGFSIDLMNAIASAANLKVNFQSLPFDGIIPALQSRTVDAAISSITITAERAETVAF 110
           G+  GF  +L+ AIA+   L++ F    F G++  + +   D   SSIT T ER +TV F
Sbjct: 94  GSFTGFDNELLKAIAAKLKLRIQFSGTEFSGLLSQVANNRFDVGSSSITTTDERRKTVDF 153

Query: 111 SRPYFKAGLAIAIRSSNEDITGFDSL-KNKKIAVQIGTTGAGKAKSIPGAQIRSFDSAPL 169
           +  Y   G    +  +   I GF +L K+ +I V  GT      ++    +   F     
Sbjct: 154 TNGY-DFGYFSLVAPAGGSIKGFANLSKSTRIGVVQGTVQDDYVQNTLHLEAVKFPDYAT 212

Query: 170 ALQELLNNNVDAVINDAPVTLYAINTGNLQGIKVVEKLLT-EEYYGIATAQNSPYLA-LI 227
           A   L +  +DA +  +     AI  G+  G  + E   +   +   A  +N P L   +
Sbjct: 213 AYANLKSGQIDAWVAPSQQAEGAIRPGD--GTTIAENTFSVNNFVAWAVGKNKPKLTEAL 270

Query: 228 NDGLNRVLADGSYSQIYQKWFKVE-------------PPSLPDKSLY--ENQTNTHKSG- 271
           N GL+ ++ADG+Y+++Y  W   E              P LPD +    EN+    K+  
Sbjct: 271 NSGLDAIIADGTYAKLYTDWVPRELPKGWKPGSKAAPAPRLPDIAAIARENEAKAPKTDN 330

Query: 272 ----------------SINLILQFLPTLLQGALV-TIQLTILSTVLGLICGTLIALTRLS 314
                           S +L  + LP LL+  L  T+ L+++S VLG I G ++A+  +S
Sbjct: 331 AAKPKSTLQQLGTTFFSWDLYAKALPDLLKTGLPNTLILSVVSGVLGTILGMVLAVAGIS 390

Query: 315 QFTPARLFARAYVDFFRGTPLLVQIFMIYFGIPALAQQLGFTFNFDRWVAGVIALSVNAA 374
           +    R  AR Y D FRG P +V I ++  GI  + + L  T N   W+ G +AL++ AA
Sbjct: 391 RSRWLRWPARIYTDIFRGLPAVVVILVVGLGIGPVVKNL--TGNNPYWL-GAVALALLAA 447

Query: 375 AYIAEIVRAGIQSIETGQTEAAKSLGLNPWLTMRLVIFPQAFRRMLPPLGNEFISLLKDT 434
           AYI EI R+GIQS++ GQ EA++++G +   +MRLV+ PQ  RR+LP L N+FISL+KD+
Sbjct: 448 AYIGEIFRSGIQSVDDGQLEASRAIGFSYRQSMRLVVVPQGVRRVLPALMNQFISLIKDS 507

Query: 435 SLVAVIGF----EELFRKGQLIVADNYRAFEIYAAVAIVYLCLTLLASQVLSRLE 485
           SLV  +G      ELF  G+ + A       + AA  ++YL LT+  + +++ ++
Sbjct: 508 SLVYFLGLLASQRELFAVGRDLNAQTGNLSPLVAA-GLIYLVLTIPLTHLVNYID 561


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: 662
Number of extensions: 40
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: 589
Length adjustment: 35
Effective length of query: 466
Effective length of database: 554
Effective search space:   258164
Effective search space used:   258164
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