GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Cupriavidus basilensis 4G11

Align High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate RR42_RS00195 RR42_RS00195 ABC transporter permease

Query= TCDB::P21627
         (307 letters)



>FitnessBrowser__Cup4G11:RR42_RS00195
          Length = 309

 Score =  182 bits (461), Expect = 1e-50
 Identities = 98/308 (31%), Positives = 170/308 (55%), Gaps = 13/308 (4%)

Query: 9   QQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGLDSV 68
           Q + NGL +G  YA++A+G+T+ +G++ +I F+HG+  M+G++    A T + M+ + S 
Sbjct: 6   QYVFNGLMLGMIYAMVAVGFTLFFGVLDVIKFSHGDTLMVGAFAGLAASTGVLMLDIQSP 65

Query: 69  PLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAVML--SQD 126
            + +LA    +I VT   G +I +    PLR    L  L++ + +   ++ +V L     
Sbjct: 66  WIRLLAVVLCAICVTGLLGAAIAKFLILPLRKAAPLNTLLATLMLGTVMRESVRLFYPDG 125

Query: 127 SKEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGRACRAC 186
           S  K  P LLP   +     +  + +    +++      ++ G+ L I+R+R G A RA 
Sbjct: 126 SNPKPFPALLPTASI----ELGSLSLRADNLILLATGIAIIVGVHLLITRTRFGMAIRAV 181

Query: 187 AEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAFTAAV 246
           A+D +   L+GIN   ++ LTF +G+ +AA+A V+ G+ Y  IN  +G L G+  F AA+
Sbjct: 182 AQDGETARLMGINFEAVVLLTFALGSGMAALAGVMNGLYYNEINFNVGLLLGVIGFAAAI 241

Query: 247 LGGIGSIPGAMLGGLLLGVAEAFGADV-------FGDQYKDVVAFGLLILVLLFRPTGIL 299
           LGG+G+I GA+LGG L    +  G+             YKDV AF ++I+++ ++PTG++
Sbjct: 242 LGGLGNIYGAILGGFLFAALQVLGSATLPALIPDIPSAYKDVFAFAVVIVLMAWKPTGLI 301

Query: 300 GRPEVEKV 307
                E+V
Sbjct: 302 AEKSSERV 309


Lambda     K      H
   0.328    0.145    0.413 

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: 291
Number of extensions: 12
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: 307
Length of database: 309
Length adjustment: 27
Effective length of query: 280
Effective length of database: 282
Effective search space:    78960
Effective search space used:    78960
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