GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natD in Amycolatopsis halophila YIM 93223

Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_034268201.1 AMYHA_RS04370 branched-chain amino acid ABC transporter permease

Query= TCDB::P74318
         (286 letters)



>NCBI__GCF_000504245.1:WP_034268201.1
          Length = 291

 Score =  127 bits (318), Expect = 4e-34
 Identities = 84/289 (29%), Positives = 155/289 (53%), Gaps = 18/289 (6%)

Query: 3   LSQLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFMTLAAYLTW-WANTSGINLWL 61
           L Q +FNG+  GS  AL A+GL++ +G+L + NFAHG F  L A+  +   +++G++ WL
Sbjct: 4   LLQQLFNGLVSGSFYALLALGLSVIFGMLGVVNFAHGAFYMLGAFGAFVLLDSAGLSWWL 63

Query: 62  SMA-----LGCVGTIIA-MFIGEWLLWKPMRARRATATTLIIISIGLALFLRNGILLIWG 115
           ++      LG +G ++  +F+   +   P+           +++ G+AL L++ I + +G
Sbjct: 64  ALLVVPILLGVIGMVLERLFVHRLMHLFPLYN--------FLLTFGIALILQDLIRMKYG 115

Query: 116 GNNQNYRVPIV--PAQDFMGIKFEYYRLLVIAMAIAAMVVLHLILQRTKVGKAMRAVADN 173
             +Q Y  P +   + D     +  Y++ V   +IA   ++ L+L RT+VG  +RA  + 
Sbjct: 116 VTSQPYARPSILDGSVDLGLFTYPKYQVFVFVFSIALSGLVWLVLSRTRVGMIVRASTER 175

Query: 174 VDLAKVSGINVEWVVMWTWVMTAVLTALGGSMYGLMTTLKPNMGWFLILPMFASVILGGI 233
            +L +  GI+V   V   +     L  L G +   M  +  +MG  LI+ +FA V++GG+
Sbjct: 176 AELTQSLGIDVRRWVTPVFGFGIALAGLAGVLAAPMRAVNSSMGADLIIVIFAVVVIGGL 235

Query: 234 GNPYGAIAGGIIIGVAQEVSVPWFGTSYKMGVALLLMIIILFIRPQGLF 282
           G+  G++A G I+G+   +   ++  +    +  +LM ++L +RP GLF
Sbjct: 236 GSVLGSVAAGYIVGMVTAIG-NFYVPALSQSLVFVLMALVLLLRPAGLF 283


Lambda     K      H
   0.329    0.143    0.450 

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: 234
Number of extensions: 18
Number of successful extensions: 3
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: 286
Length of database: 291
Length adjustment: 26
Effective length of query: 260
Effective length of database: 265
Effective search space:    68900
Effective search space used:    68900
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 (21.8 bits)
S2: 48 (23.1 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