GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natD in Magnetospirillum magneticum AMB-1

Align NatD, 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_043743902.1 AMB_RS08455 branched-chain amino acid ABC transporter permease

Query= TCDB::Q8YXD0
         (288 letters)



>NCBI__GCF_000009985.1:WP_043743902.1
          Length = 291

 Score =  143 bits (360), Expect = 5e-39
 Identities = 87/283 (30%), Positives = 154/283 (54%), Gaps = 9/283 (3%)

Query: 6   IQLIVNGIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGAYLTFFVNTFGVNIWLSM 65
           +Q + +G+  G+I ALA +G  + Y    + NFA G+F+ +G   T  +   GV I+L++
Sbjct: 6   LQYLFSGLTSGAIYALAGLGFAIIYNASHVINFAQGEFIMIGGMATATMVAAGVPIYLAI 65

Query: 66  IVAVVGTVGVMLLSEKLLWSRMRSIRANSTTLIIISIGLALFLRNGIILIWGGRNQNYNL 125
            +A+  ++ V +  EK      R+  A+  T+III+IG ++F+R    LIW    + ++L
Sbjct: 66  PLAMAASMLVGVAMEKFAIEPARN--ADVVTIIIITIGASIFMRGAAQLIWD--KEFHSL 121

Query: 126 PI----TPALDIFGVKVPQNQLLVLALAVLSIGALHYLLQNTKIGKAMRAVADDLDLAKV 181
           P     TP + + G  +    L V  ++ ++I  L Y    T  GKAM   + +   A++
Sbjct: 122 PAFSGETP-IAVMGATLMPQSLWVFGISAVAIALLWYFFNRTMFGKAMLGTSHNRLAAQL 180

Query: 182 SGIDVEQVIFWTWLIAGTVTSLGGSMYGLITAVRPNMGWFLILPLFASVILGGIGNPYGA 241
            G+ V++V+  ++ ++  + ++GG +   IT      G  L L  F++ +LGG+GN  GA
Sbjct: 181 VGVAVKRVLLASFALSALLGAVGGIVVTPITFTNYEAGIMLGLKGFSAAVLGGLGNGTGA 240

Query: 242 IAAAFIIGIVQEVSTPFLGSQYKQGVALLIMILVLLIRPKGLF 284
           I    I+GI + +++ +L S YK  +A +I++ VL   P GLF
Sbjct: 241 IIGGLIVGIAEAMASGYLSSAYKDAIAFIIILFVLFFMPSGLF 283


Lambda     K      H
   0.328    0.144    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: 222
Number of extensions: 12
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: 288
Length of database: 291
Length adjustment: 26
Effective length of query: 262
Effective length of database: 265
Effective search space:    69430
Effective search space used:    69430
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: 48 (23.1 bits)

This GapMind analysis is from Sep 17 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