GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Pseudomonas fluorescens FW300-N2E3

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 AO353_13345 AO353_13345 branched-chain amino acid transporter permease subunit LivH

Query= TCDB::P21627
         (307 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_13345
          Length = 304

 Score =  330 bits (845), Expect = 3e-95
 Identities = 165/301 (54%), Positives = 222/301 (73%), Gaps = 1/301 (0%)

Query: 7   YLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGLD 66
           +LQQ++NGLT+GS Y LIAIGYTMVYGIIGMINFAHGEVYMI +Y+A I++ LL+  G++
Sbjct: 5   FLQQVINGLTLGSVYGLIAIGYTMVYGIIGMINFAHGEVYMISAYLAAISLALLSYFGVE 64

Query: 67  SVPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAVMLSQD 126
           S PL++L     ++ VT  +G+ IER+AY+PLR   RL PLISAIG+S+ LQN   ++Q 
Sbjct: 65  SFPLLILGTLLFTVFVTGVYGWVIERIAYKPLRNSTRLAPLISAIGVSLILQNYAQIAQG 124

Query: 127 SKEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGRACRAC 186
           S+++ IPTLL G   F +     V I+Y +I I V  F+ M  LT  I  ++LGR CRA 
Sbjct: 125 SRQQGIPTLLSGGLRF-DIGTGFVQITYTKIFILVAAFIGMALLTYIIKYTKLGRMCRAT 183

Query: 187 AEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAFTAAV 246
            +D KM ++LGIN++ +I+  F+IGAA+AA+A VL+ + YG  +   GF+ GIKAFTAAV
Sbjct: 184 QQDRKMASILGINTDRVISYVFIIGAAMAALAGVLITVNYGTFDFYAGFVIGIKAFTAAV 243

Query: 247 LGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGILGRPEVEK 306
           LGGIGS+PGAMLGG++LGV+E+  + V    YKDV +F LL+L+L+FRP G+LGRP V K
Sbjct: 244 LGGIGSLPGAMLGGIILGVSESLFSGVINSDYKDVFSFSLLVLILIFRPQGLLGRPLVAK 303

Query: 307 V 307
           V
Sbjct: 304 V 304


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: 367
Number of extensions: 14
Number of successful extensions: 2
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: 304
Length adjustment: 27
Effective length of query: 280
Effective length of database: 277
Effective search space:    77560
Effective search space used:    77560
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