GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Bacillus altitudinis 41KF2b

Align NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate WP_035702265.1 BA79_RS08570 sugar ABC transporter ATP-binding protein

Query= TCDB::Q8YT15
         (247 letters)



>NCBI__GCF_000691145.1:WP_035702265.1
          Length = 493

 Score =  113 bits (282), Expect = 8e-30
 Identities = 65/215 (30%), Positives = 119/215 (55%), Gaps = 7/215 (3%)

Query: 12  LEVENVHAGYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKITF 71
           +E+ N+H  + K+  +L GV+F + +GE+  ++G NGAGKSTL   + GL +   G I  
Sbjct: 3   IEMHNIHKAFGKNT-VLAGVSFDLVTGEVHALMGENGAGKSTLMNLLTGLYSLDQGTIQI 61

Query: 72  KGKNIAGLKSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRND----SLQPLKDKIF 127
            GK  A     +  + G+ ++ Q  N++P ++V ENL +G  I         + +K    
Sbjct: 62  DGKETAFKNPKEAEQNGIAFIHQELNIWPDMTVLENLFIGKEIYTKLGLLDTKKMKALAQ 121

Query: 128 AMFPRLSDRRR--QRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQ 185
           A   RLS      Q AG+ S G++QM+ + KALM +  ++++DEP+AAL+   + ++F+ 
Sbjct: 122 AQLDRLSVNLSLDQEAGSCSVGQKQMIEIAKALMTDAKVIIMDEPTAALTDREIEKLFQV 181

Query: 186 VKQINQEGTAIILVEQNARKALEMADRGYVLESGR 220
           ++ + +EG +I+ +     +   + DR  ++  G+
Sbjct: 182 IESLKKEGVSIVYISHRMEEIFAICDRITIMRDGK 216



 Score = 82.4 bits (202), Expect = 2e-20
 Identities = 60/215 (27%), Positives = 107/215 (49%), Gaps = 27/215 (12%)

Query: 29  QGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKITFKGKNIAGLKSNQIVRLG 88
           Q V+F V++GE+V V G  GAG++ + +++FGL     G+I   GK     K +  V+LG
Sbjct: 268 QDVSFSVKAGEIVGVAGLMGAGRTEMMRSLFGLDPLDQGEIWVHGKKAVIKKPSDAVKLG 327

Query: 89  MCYVPQIANVFPSLSVEENLEMGAFIRN-------DSLQPL--------KDKIFAMFPRL 133
           + ++ +          +E L + A IR        DS  P         +D +  +  RL
Sbjct: 328 IGFITEDRK-------DEGLMLDASIRENIGLPNLDSFSPKGLIDKKNEQDFVDLLIKRL 380

Query: 134 SDRRRQR---AGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVKQIN 190
           + +       A +LSGG +Q + + K + ++P +L+LDEP+  +      ++++ + ++ 
Sbjct: 381 TIKTASSEISARSLSGGNQQKVVIAKWIGIQPKVLILDEPTRGVDVGAKREIYQLMNELT 440

Query: 191 QEGTAIILVEQNARKALEMADRGYVLESGRDAISG 225
             G AI++V     + L M+DR  V+  G   ISG
Sbjct: 441 DRGVAILMVSSELPEVLGMSDRVLVIHEG--TISG 473


Lambda     K      H
   0.317    0.136    0.377 

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: 319
Number of extensions: 19
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 247
Length of database: 493
Length adjustment: 29
Effective length of query: 218
Effective length of database: 464
Effective search space:   101152
Effective search space used:   101152
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 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