GapMind for catabolism of small carbon sources

 

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

Align ABC transporter permease (characterized, see rationale)
to candidate WP_011385948.1 AMB_RS18170 branched-chain amino acid ABC transporter permease

Query= uniprot:A0A165KC95
         (309 letters)



>NCBI__GCF_000009985.1:WP_011385948.1
          Length = 297

 Score =  164 bits (415), Expect = 2e-45
 Identities = 94/306 (30%), Positives = 167/306 (54%), Gaps = 14/306 (4%)

Query: 3   ILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMP 62
           +LLQ ++NGL++G++Y ++A+ + ++Y   Q++NFA GE L+IGA T W  +  M     
Sbjct: 5   LLLQLLVNGLIVGTLYGVVAMCFVLIYKSTQVVNFAQGEFLLIGAWTCWWLVTSM----- 59

Query: 63  GAPGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAMII 122
             P +V   +  +   V    L  ++     RPL   P ++ ++  IG+SI  Q +   I
Sbjct: 60  ALPFYVAFPMTFLFMMVFGIALQMIV----LRPLIGEPVISVIMVTIGLSIFFQAVMKSI 115

Query: 123 WKPNYKPYPTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRATAE 182
           +    +P+P + P    +I G  + P  ++ L V+ V +    +   ++ +G AMRATA 
Sbjct: 116 FGVWAQPFPEIFPVKSVDILGLSVQPAYLMSLVVSIVIMGLFAWFFKYSRMGLAMRATAF 175

Query: 183 NPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAVFG 242
           N +VA  +G+    V +  + I A+++A+AG++     G +     F  G+K F A + G
Sbjct: 176 NQQVAQSLGISVKAVFATAWAISAMVSALAGVVVGMVNGVSSALSFF--GIKVFPAVIVG 233

Query: 243 GIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGLLG 302
           G+ ++ GAV+GG+++G++E +     G      LG+ YT +  F VL+IIL ++P GL G
Sbjct: 234 GLDSIIGAVLGGLIIGVLENLAEYADGQYLH--LGNLYT-VAPFYVLVIILMIKPYGLFG 290

Query: 303 ERVADR 308
            +  +R
Sbjct: 291 TKTIER 296


Lambda     K      H
   0.327    0.142    0.419 

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: 215
Number of extensions: 7
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: 309
Length of database: 297
Length adjustment: 27
Effective length of query: 282
Effective length of database: 270
Effective search space:    76140
Effective search space used:    76140
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