GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Pseudomonas stutzeri RCH2

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 GFF3786 Psest_3855 Branched-chain amino acid ABC-type transport system, permease components

Query= TCDB::P21627
         (307 letters)



>FitnessBrowser__psRCH2:GFF3786
          Length = 295

 Score =  140 bits (352), Expect = 5e-38
 Identities = 92/300 (30%), Positives = 160/300 (53%), Gaps = 17/300 (5%)

Query: 4   IYHYLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLLAMM 63
           I  +L QL+ GL  GS YA++++G  +++G++ +INFAHG  YMIG++  ++   LLA +
Sbjct: 9   IQAFLGQLLIGLINGSFYAMLSLGLAIIFGMLKIINFAHGAQYMIGAFAGYL---LLATL 65

Query: 64  GLDSVPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNA--V 121
           G+   P ++LA      I+       IER+A   L   + L  L+   G+++ L+ A   
Sbjct: 66  GIGYWPALILAP-----IIVGLCSAVIERLALSRLYNLDHLYSLLFTFGLALALEGAFRY 120

Query: 122 MLSQDSKEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLGR 181
                 +  A+P  L G +     ++  + +   +  + + + ++     L I +++LG 
Sbjct: 121 FYGSSGQPYAVPKELAGGY-----NLGFMFLPKYRAWVVLASLVICIASWLLIEKTKLGA 175

Query: 182 ACRACAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIKA 241
             RA  E+  +    GIN   ++  T+ +GAALA +A +L    Y V +P +G    I  
Sbjct: 176 YLRAATENPTLVRTFGINVPLLLTFTYGMGAALAGLAGMLAAPIYQV-SPLMGSNLIIVV 234

Query: 242 FTAAVLGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGILGR 301
           F   V+GG+GSI GA++ G +LG+ E     VF  +  ++V F ++ +VLL RP G++GR
Sbjct: 235 FAVVVVGGMGSILGAIITGYMLGILEGL-TKVFYPEASNIVIFVIMAIVLLVRPAGLMGR 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: 290
Number of extensions: 18
Number of successful extensions: 5
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