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_011384432.1 AMB_RS10245 branched-chain amino acid ABC transporter permease

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



>NCBI__GCF_000009985.1:WP_011384432.1
          Length = 289

 Score =  141 bits (355), Expect = 2e-38
 Identities = 88/303 (29%), Positives = 161/303 (53%), Gaps = 27/303 (8%)

Query: 7   YFLQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMGI 66
           +F+  +  G+  G  Y L+A+G ++++G++ ++NFAHG++ ++  Y +F++   L +  +
Sbjct: 5   FFVNVISAGLLTGLVYGLMALGLSVIFGVMRVVNFAHGDMMVVAMYAAFLLFTKLGIEPV 64

Query: 67  DTGWLLVAAGFVGAIVIASAYGWSIERVAYRPVRNSKRLIALISAIGMSIFLQNYVSLTE 126
               L+    FV         G+ ++R            I  +  + +++ + N V +  
Sbjct: 65  PALPLVAGGLFV--------VGYLLQRFLINHFLGVTEHIQFLLLLSVAMIITNVVLMVF 116

Query: 127 G--SRDVALPSLF---NGQWVVGHSENFSASITT--MQAVIWIVTFLAMLALTIFIRYSR 179
           G  +R++ L + F   N  W+V       A+ T   + A++W            F RY+ 
Sbjct: 117 GPDARNIQLDASFESYNLGWLVLDKVRVIAAFTAGGVAALLWA-----------FFRYTT 165

Query: 180 MGRACRACAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAG 239
            G A RACA++   A ++G++ +++ A+TF IG A    AG LL     V +P++     
Sbjct: 166 TGTAIRACADNPVGARVVGLDVEKLYAITFGIGTACVGAAGCLLLLLVDV-HPHLSSDYT 224

Query: 240 MKAFTAAVLGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVMPTGI 299
           +  F   +LGG+GS+ GA++GG+++G++EALS   ++   K + SF LLILVLL+ P GI
Sbjct: 225 LLGFIIVILGGLGSLGGALLGGILVGLSEALSGVLIAPSLKSMFSFGLLILVLLLRPQGI 284

Query: 300 LGR 302
           LG+
Sbjct: 285 LGK 287


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: 235
Number of extensions: 9
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: 308
Length of database: 289
Length adjustment: 27
Effective length of query: 281
Effective length of database: 262
Effective search space:    73622
Effective search space used:    73622
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