GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Sinorhizobium meliloti 1021

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 SMc03118 SMc03118 ABC transporter permease

Query= TCDB::P21627
         (307 letters)



>FitnessBrowser__Smeli:SMc03118
          Length = 295

 Score =  149 bits (377), Expect = 6e-41
 Identities = 98/297 (32%), Positives = 164/297 (55%), Gaps = 17/297 (5%)

Query: 7   YLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGLD 66
           +L QL+ GL  GS YAL+++G  +++G++ +INFAHG  YM+G+++A++   LL+ +G+ 
Sbjct: 12  FLGQLLIGLINGSFYALLSLGLAIIFGLLRVINFAHGAQYMLGAFMAWL---LLSYLGIG 68

Query: 67  SVPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNA--VMLS 124
             P ++LA     +I     G  IER   R L   + L  L+   G+++ ++     +  
Sbjct: 69  YWPALILAPLLVGLI-----GAVIERTMLRRLYTLDPLYGLLFTFGLALTIEGTFRYLYG 123

Query: 125 QDSKEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGRACR 184
              +  A P LL      G +++  + +   +  + V + ++  G  L I +++LG   R
Sbjct: 124 ASGQPYATPALL-----MGGANLGFMFLPIYRGWVIVFSLVICLGTWLMIEKTKLGSYLR 178

Query: 185 ACAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAFTA 244
           A  E+  +    GIN   ++ LT+ +GAALAA+A VL    Y V +P +G    I  F  
Sbjct: 179 AATENPVLVQSFGINVPFLLTLTYGLGAALAAIAGVLAAPIYQV-SPLMGSNIIIVVFAV 237

Query: 245 AVLGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGILGR 301
            V+GG+GSI GA++ G LLG+AE     VF  +  ++V F ++ +VLL RP G+ GR
Sbjct: 238 VVVGGMGSIMGAIVTGYLLGIAEGL-TKVFYPEASNIVIFVIMAIVLLLRPAGLFGR 293


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: 310
Number of extensions: 17
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: 295
Length adjustment: 27
Effective length of query: 280
Effective length of database: 268
Effective search space:    75040
Effective search space used:    75040
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