GapMind for catabolism of small carbon sources

 

Alignments for a candidate for alsT in Brucella inopinata BO1

Align Amino-acid carrier protein, AlsT (characterized)
to candidate WP_008510473.1 BIBO1_RS17340 sodium:alanine symporter family protein

Query= TCDB::Q45068
         (465 letters)



>NCBI__GCF_000182725.1:WP_008510473.1
          Length = 477

 Score =  424 bits (1089), Expect = e-123
 Identities = 225/472 (47%), Positives = 317/472 (67%), Gaps = 19/472 (4%)

Query: 7   SLINIPSDFIWKY-LFYILIGLGLFFTIRFGFIQFRYFIEMFRIV---GEKPEGNKGVSS 62
           ++I+  ++  W Y L Y L+ +G FFTIR  F+QF +F E+FR+V   G + E   G+S 
Sbjct: 3   TIIDFLNNVFWNYILVYGLLAVGFFFTIRLKFVQFVHFPELFRVVFAAGRRDEA--GISP 60

Query: 63  MQAFFISAASRVGTGNLTGVALAIATGGPGAVFWMWVVAAVGMASSFVESTLAQLYKVRD 122
            QA  IS ASRVGTGN+TGVA+A+  GGPGA+FWMW+VA VG+A+++ ES LAQLYK+R+
Sbjct: 61  FQALTISIASRVGTGNITGVAVALYLGGPGAIFWMWIVALVGLATAYSESALAQLYKIRN 120

Query: 123 GE-DFRGGPAYYIQKGLGARWLGIVFAILITVSFGLIFNAVQTNTIAGALDGAFHVNKIV 181
            +  +RGGPA+YI +GLG  W G +F++ + +SFGL+FNAVQ N IA ++  AF++ K+ 
Sbjct: 121 QDGQYRGGPAFYIARGLGLPWAGALFSVCLILSFGLVFNAVQANAIADSMVMAFNMPKLG 180

Query: 182 VAIVLAVLTAFIIFGGLKRVVAVSQLIVPVMAGIYILIALFVVITNITAFPGVIATIVKN 241
             IVLA+L+  +IFGG++++  V++++VP MA  YIL+A+ ++  N  A P  IA I  +
Sbjct: 181 TGIVLAILSGVVIFGGIRQIARVAEVVVPFMAFAYILMAICILAINFQAVPSTIALIFSS 240

Query: 242 ALGFEQVVGGGIGGI---IVIGAQRGLFSNEAGMGSAPNAAATAHVS--HPAKQGFIQTL 296
           A G  + VGG  GGI   ++ G +RGLFSNEAGMGSAPN AA A  +  HP+ QGF+Q+L
Sbjct: 241 AFGLHEAVGGVTGGITAAMLNGVKRGLFSNEAGMGSAPNIAAVATPAPHHPSSQGFVQSL 300

Query: 297 GVFFDTFIICTSTAFIILLYSVTPKGDGI---QVTQAALNHHIGGWAPTFIAVAMFLFAF 353
           GVF DT ++CT+TA +ILL  +   G G+   Q+TQ A+ HHIG     FIA A+F FAF
Sbjct: 301 GVFIDTILVCTATAIMILLSGILEPGSGLTGTQLTQMAMTHHIGDVGVYFIAAAIFFFAF 360

Query: 354 SSVVGNYYYGETNIEFIKT-SKTWLNIYRIAVIAMVVYGSLSGFQIVWDMADLFMGIMAL 412
           +S++GNY Y E+ + F+    K  + I R A++AMVV+G+      V+D AD  MG+MA 
Sbjct: 361 TSIIGNYSYAESAMTFLGLGGKVPITILRCALLAMVVWGAYESIHTVFDAADASMGLMAT 420

Query: 413 INLIVIALLSNVAYKVYKDYAKQRKQGLDPVFKAKNIPGLK---NAETWEDE 461
           INLI I LLS    K+  DY  QR+ G  P F A + P L+   + E W ++
Sbjct: 421 INLIAIVLLSGTVKKLTVDYFAQRRAGQVPTFHAADYPELQGQIDMEIWSEQ 472


Lambda     K      H
   0.327    0.142    0.426 

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: 591
Number of extensions: 28
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: 465
Length of database: 477
Length adjustment: 33
Effective length of query: 432
Effective length of database: 444
Effective search space:   191808
Effective search space used:   191808
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (24.3 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