GapMind for catabolism of small carbon sources

 

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

Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate WP_043743902.1 AMB_RS08455 branched-chain amino acid ABC transporter permease

Query= ecocyc::LIVH-MONOMER
         (308 letters)



>NCBI__GCF_000009985.1:WP_043743902.1
          Length = 291

 Score =  169 bits (427), Expect = 9e-47
 Identities = 101/306 (33%), Positives = 169/306 (55%), Gaps = 18/306 (5%)

Query: 5   FLYFLQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMM 64
           F  FLQ +F+G+T G+ YAL  +G+ ++Y    +INFA GE  MIG   +  ++AA + +
Sbjct: 2   FAAFLQYLFSGLTSGAIYALAGLGFAIIYNASHVINFAQGEFIMIGGMATATMVAAGVPI 61

Query: 65  GIDTGWLLVAAGFVGAIVIASAYGWSIERVAYRPVRNSKRLIALISAIGMSIFLQNYVSL 124
            +     + A+  VG          ++E+ A  P RN+  +  +I  IG SIF++    L
Sbjct: 62  YLAIPLAMAASMLVGV---------AMEKFAIEPARNADVVTIIIITIGASIFMRGAAQL 112

Query: 125 TEGSRDVALPSLFNGQWVVGHSENFSASITTMQAVIWI--VTFLAMLALTIFIRYSRMGR 182
                  +LP+ F+G+  +          T M   +W+  ++ +A+  L  F   +  G+
Sbjct: 113 IWDKEFHSLPA-FSGETPIA-----VMGATLMPQSLWVFGISAVAIALLWYFFNRTMFGK 166

Query: 183 ACRACAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAGMKA 242
           A    + +   A L+G+   RV+  +F + A + AV G+++       N   G M G+K 
Sbjct: 167 AMLGTSHNRLAAQLVGVAVKRVLLASFALSALLGAVGGIVVTPIT-FTNYEAGIMLGLKG 225

Query: 243 FTAAVLGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVMPTGILGR 302
           F+AAVLGG+G+  GA+IGGLI+GIAEA++S YLS+ YKD ++F +++ VL  MP+G+ G+
Sbjct: 226 FSAAVLGGLGNGTGAIIGGLIVGIAEAMASGYLSSAYKDAIAFIIILFVLFFMPSGLFGK 285

Query: 303 PEVEKV 308
              ++V
Sbjct: 286 RGTDRV 291


Lambda     K      H
   0.328    0.141    0.410 

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: 242
Number of extensions: 15
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: 308
Length of database: 291
Length adjustment: 27
Effective length of query: 281
Effective length of database: 264
Effective search space:    74184
Effective search space used:    74184
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 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