GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PGA1_c12660 in Magnetospirillum magneticum AMB-1

Align D-lactate transporter, permease component 2 (characterized)
to candidate WP_011385250.1 AMB_RS14465 branched-chain amino acid ABC transporter permease

Query= reanno::Phaeo:GFF1250
         (340 letters)



>NCBI__GCF_000009985.1:WP_011385250.1
          Length = 286

 Score =  194 bits (493), Expect = 2e-54
 Identities = 114/327 (34%), Positives = 171/327 (52%), Gaps = 49/327 (14%)

Query: 5   LLQILNGLDKGSAYALIALGLTLIFGTLGVVNFAHGALFMIGAFCAVTVQRVLSLSFETV 64
           L+Q+LNG+  G    L+A GLTLIFG +G++N AHGA +M+GA+ A              
Sbjct: 7   LIQVLNGVQYGLLLFLVASGLTLIFGIMGIINLAHGAFYMLGAYLAY------------- 53

Query: 65  DETQKDFLGNPLKVKTPYVESWFGPEVGGAIIDWAVPLAILFAIPIMIGVGYVMERGLIK 124
                                W     G      ++  A+L ++PI   +GY +E  L++
Sbjct: 54  ---------------------WLARTTG------SLGAAVLLSLPIAAAIGYGIEALLVR 86

Query: 125 HFYKRPHADQILVTFGLAIVLQEVVKYFYGANPIQTPAPDALNGVVNLGSIIGMDIVYPV 184
             Y+R H DQ+L+T+GL ++  E  +  +GA+      P ALN  + L   +     YPV
Sbjct: 87  TLYRRDHLDQVLLTYGLILIFNEATRMIWGADVHGVAVPAALNWSIRLTDTLS----YPV 142

Query: 185 WRVVYFFFAVVIIGGIFSFLQFTTFGMVVRAGMADRETVGLLGINIDRRFTIMFGIAAAV 244
           +R++      V+  G++  +  T FGM VRAG ++R+ V  LGIN+   F ++F + AA+
Sbjct: 143 YRLMLSGVCAVLAVGMYLVITRTRFGMWVRAGASNRDMVAALGINVKLLFGVVFALGAAL 202

Query: 245 AGLAGVMYTPINSPNYHMGMDFLVLSFVVVVVGGMGSLPGAVLAGFLLGVLESFASMNEI 304
           AGLAG + TPI S    MG   L+L FVVVV+GG+GS+ GA L   L+G+ ++F      
Sbjct: 203 AGLAGAISTPITSVAPGMGDSVLILCFVVVVIGGVGSIKGAFLGAMLIGLADTFG----- 257

Query: 305 KSLIPGIDQIIIYVVAIIILLTRPRGL 331
           K   P      +Y V   +LL +PRGL
Sbjct: 258 KVFAPDFASFTVYGVMAAVLLWKPRGL 284


Lambda     K      H
   0.329    0.147    0.439 

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: 297
Number of extensions: 14
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 340
Length of database: 286
Length adjustment: 27
Effective length of query: 313
Effective length of database: 259
Effective search space:    81067
Effective search space used:    81067
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