GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Pantoea rwandensis LMG 26275

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 WP_084935582.1 HA51_RS15840 branched-chain amino acid ABC transporter permease LivH

Query= TCDB::P21627
         (307 letters)



>NCBI__GCF_002095475.1:WP_084935582.1
          Length = 304

 Score =  327 bits (837), Expect = 3e-94
 Identities = 168/302 (55%), Positives = 221/302 (73%), Gaps = 3/302 (0%)

Query: 7   YLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGLD 66
           ++QQ++NGLT+G+ Y LIAIGYTMVYGIIGMINFAHGEVYMI +Y+  I + LL+  G+ 
Sbjct: 5   FIQQMINGLTLGAVYGLIAIGYTMVYGIIGMINFAHGEVYMISAYLCAIGLALLSYFGIH 64

Query: 67  SVPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAVMLSQD 126
           S PL++      +IIVT+A+G++IER+AYRPLR   RL PLISAIGMS+ LQN V LSQ 
Sbjct: 65  SFPLLIFGTLLFTIIVTAAYGWAIERIAYRPLRNSTRLAPLISAIGMSLILQNYVQLSQG 124

Query: 127 SKEKAIPTLLPGNFVFGESSMNGVV-ISYMQILIFVVTFLVMFGLTLFISRSRLGRACRA 185
             ++ IPTL+ G  V       G+V I++ ++ I +  F  M  LT  I  ++LGR CRA
Sbjct: 125 PNQQGIPTLMTG--VLRMEIDGGIVQITWTKVFILIAAFCGMAFLTWIIQYTKLGRICRA 182

Query: 186 CAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAFTAA 245
             +D +M ++LGIN++ +I+L FV+GAA+A +A VL+ M YG  +   GF+ GIKAFTAA
Sbjct: 183 VQQDRRMASILGINTDRVISLVFVMGAAMAGLAGVLVTMNYGTFDFYAGFIIGIKAFTAA 242

Query: 246 VLGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGILGRPEVE 305
           VLGGIGS+PGAMLGGLLLGVAEA  A +    YKDV +F LL+++L+FRP G+LGRP V 
Sbjct: 243 VLGGIGSLPGAMLGGLLLGVAEAQFAGLVNSDYKDVFSFALLVVILIFRPQGLLGRPLVA 302

Query: 306 KV 307
           KV
Sbjct: 303 KV 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: 350
Number of extensions: 16
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 24 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