GapMind for catabolism of small carbon sources

 

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

Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate WP_043745123.1 AMB_RS18175 branched-chain amino acid ABC transporter permease

Query= TCDB::Q8DQH9
         (318 letters)



>NCBI__GCF_000009985.1:WP_043745123.1
          Length = 356

 Score =  150 bits (378), Expect = 6e-41
 Identities = 95/303 (31%), Positives = 159/303 (52%), Gaps = 32/303 (10%)

Query: 30  VLNLFYVQILQQIGINIILAVGLNLIVGFSGQFSLGHAGFMAIGAYAAAIIGSKSPTYGA 89
           VL+ + + +L QIG   I A+GLN++VG +GQ SLGHA F   GA+A+A + +   T+G 
Sbjct: 45  VLSNYLLALLIQIGFYGIAALGLNILVGCTGQISLGHAAFFGFGAFASAWLNN---TFGV 101

Query: 90  -FFGAMLVGALLSGAVALLVGIPTLRLKGDYLAVATLGVSEIIRIFIINGGSLTNGAAGI 148
               A+ +  +++  + LL GIP  RLKG YLA+AT     I+  F       T G++G 
Sbjct: 102 PVLLAIPLAGVMTTLLGLLFGIPAGRLKGLYLAIATFASQFILEDFFARANWFTGGSSGA 161

Query: 149 LGIP----------NFTTWQMVYFFVVITTIATLNFLRSPIGRSTLSVREDEIAAESVGV 198
           +  P          +   + +V  FVV+  +   N LR+  GR+ ++VR+  ++AE +G+
Sbjct: 162 MANPISLFGYEVGGDKGFFYVVLVFVVVMYVLGTNLLRTRDGRAFVAVRDHYLSAEVMGI 221

Query: 199 NTTKIKIIAFVFGAITASIAGSLQAGFIGSVVPKDYTFINSINVLIIVVFGGLGSITGAI 258
           N TK +I++F   +  A + G+L   ++G V  + +T + SI  L +++ GG+GS+ G +
Sbjct: 222 NLTKYRILSFGISSFYAGVGGALYGHYLGYVSAEGFTILLSIQFLGMIIIGGMGSVMGTL 281

Query: 259 VSAIVL------------------GILNMLLQDVASVRMIIYALALVLVMIFRPGGLLGT 300
           +    +                  G +  L   +A ++     LA+VL +IF P GL+  
Sbjct: 282 MGTAFMVLLPEATEAAVSTVKHFTGDIPALTSALAYIKEATIGLAIVLFLIFEPDGLVHR 341

Query: 301 WEL 303
           W L
Sbjct: 342 WRL 344


Lambda     K      H
   0.327    0.143    0.403 

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: 265
Number of extensions: 18
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: 318
Length of database: 356
Length adjustment: 28
Effective length of query: 290
Effective length of database: 328
Effective search space:    95120
Effective search space used:    95120
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 (21.6 bits)
S2: 49 (23.5 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