GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PGA1_c12660 in Acidovorax sp. GW101-3H11

Align D-lactate transporter, permease component 2 (characterized)
to candidate Ac3H11_68 High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1)

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_68
          Length = 328

 Score =  140 bits (354), Expect = 3e-38
 Identities = 99/322 (30%), Positives = 156/322 (48%), Gaps = 39/322 (12%)

Query: 11  GLDKGSAYALIALGLTLIFGTLGVVNFAHGALFMIGAFCAVTVQRVLSLSFETVDETQKD 70
           GL  G    +IA GLTL+FG + V+NF HG    +GAF A +V   +       D TQ  
Sbjct: 39  GLAMGMIIFIIASGLTLVFGLMDVLNFGHGVFIALGAFVATSVLGAMG------DYTQSA 92

Query: 71  FLGNPLKVKTPYVESWFGPEVGGAIIDWAVPLAILFAIPIMIGVGYVMERGLIKHFYKRP 130
            L   L    P                     A+L A+ +   VG   ER +++  Y + 
Sbjct: 93  DLWRNLMAVLP---------------------AMLVAMAVAGAVGLAFERFIVRPVYGQ- 130

Query: 131 HADQILVTFGLAIVLQEVVKYFYGANPIQTPAPDALNGVVNLGSIIGMDIVYPVWRVVYF 190
           H  QIL+T G  I+ +E +K  +G   I  P P+ + G + +G     D     +R++  
Sbjct: 131 HLKQILITMGGMIIGEEFIKVIWGPQQIPLPLPEGMRGSLLVG-----DAAIEKYRLLAM 185

Query: 191 FFAVVIIGGIFSFLQFTTFGMVVRAGMADRETVGLLGINIDRRFTIMFGIAAAVAGLAGV 250
              +++ G +   L  T  G+++RAG+ DRE V  LG  I R F  +F + +A+AGL GV
Sbjct: 186 AVGLLVFGVLAWTLSRTKVGLLIRAGVQDREMVESLGYRIRRLFIGVFVVGSALAGLGGV 245

Query: 251 MYTPI-NSPNYHMGMDFLVLSFVVVVVGGMGSLPGAVLAGFLLGVLESFASMNEIKSLIP 309
           M+     S    MG    VL F+V+++GG+GS  GA++   L+G++ ++        L+P
Sbjct: 246 MWGLYQQSVVPQMGAQVNVLIFIVIIIGGLGSTGGALIGALLVGLMANYTGF-----LVP 300

Query: 310 GIDQIIIYVVAIIILLTRPRGL 331
            +       + + ILL RP+G+
Sbjct: 301 KVALFSNITLMVAILLWRPQGV 322


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: 272
Number of extensions: 19
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: 340
Length of database: 328
Length adjustment: 28
Effective length of query: 312
Effective length of database: 300
Effective search space:    93600
Effective search space used:    93600
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: 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