GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Desulfovibrio vulgaris Hildenborough

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 206138 DVU0713 branched-chain amino acid ABC transporter, permease protein

Query= TCDB::P21627
         (307 letters)



>MicrobesOnline__882:206138
          Length = 301

 Score =  262 bits (670), Expect = 6e-75
 Identities = 141/301 (46%), Positives = 196/301 (65%), Gaps = 3/301 (0%)

Query: 7   YLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMMGLD 66
           +LQQL NGL VG  YALIA+GYTMVYG++ +INFAHG+++ IG+Y+ F     L + G  
Sbjct: 4   FLQQLTNGLAVGGIYALIALGYTMVYGVLKLINFAHGDLFTIGAYLGFTVFAALGLSGHV 63

Query: 67  SVPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNAVMLSQD 126
           S  + +L      + + +  GY +ERVAYRPLR  +RL  ++SA+G SIF QNAVML   
Sbjct: 64  SGAVAVLLVTTMVMGLVALIGYLLERVAYRPLRSSSRLSAVVSALGASIFFQNAVMLIYG 123

Query: 127 SKEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGRACRAC 186
           +K +  P  +         S  G+ I  ++I++F  +  +M  L  FI R+R G A RA 
Sbjct: 124 AKFQVYPNDIRPTMAV---SFFGMDIPLVRIMMFGASVALMLLLHFFIHRTRTGTAIRAV 180

Query: 187 AEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKAFTAAV 246
           A D     L+GI+ N +IAL F+IG AL   A V++G+ YG I+  +G++ G+KAFTAA+
Sbjct: 181 AIDQGAAKLMGIDVNRVIALVFMIGPALGGAAGVMVGLYYGQIDFTMGWVYGLKAFTAAI 240

Query: 247 LGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGILGRPEVEK 306
           LGGIG+IPGAM+GGLLLGV EA GA      +KD +AF +LIL+L+ RPTG+LG    +K
Sbjct: 241 LGGIGNIPGAMVGGLLLGVIEALGAAYISIAWKDAIAFLVLILILIIRPTGLLGERVADK 300

Query: 307 V 307
           +
Sbjct: 301 I 301


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: 333
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: 301
Length adjustment: 27
Effective length of query: 280
Effective length of database: 274
Effective search space:    76720
Effective search space used:    76720
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