GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braE in Pseudomonas putida KT2440

Align High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate PP_4865 PP_4865 High-affinity branched-chain amino acid transport system permease protein BraE

Query= TCDB::P21628
         (417 letters)



>FitnessBrowser__Putida:PP_4865
          Length = 435

 Score =  407 bits (1047), Expect = e-118
 Identities = 214/414 (51%), Positives = 286/414 (69%), Gaps = 12/414 (2%)

Query: 1   MSQSLKRALFSALLVILVSYPILGLKLRTVGIKLEVLGADAQTLWTIAAAALAMFVWQLF 60
           + +SL   + + LL ++V  P++G+ L       E      +  W +    +  F+  LF
Sbjct: 19  LKRSLLETIVAGLLALIVFGPVVGVVLDGYTFNAE----PRRVAWLVGGVMVGRFLLSLF 74

Query: 61  RDRIPLKLGRGVGYKVNGSGLKNFLSLP---STQRWAVLALVVVAFVWPFFASRGAVDIA 117
               P +    +G+   GSG+   ++ P   S  R+ + AL+V+A V+P FA++  + + 
Sbjct: 75  LQTAPGQRML-LGFDSGGSGVH--VTAPDYKSRLRYIIPALIVIAIVFPIFANKYLLTVV 131

Query: 118 TLILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYTYALLAEYAGFGFWTALPIAGMMA 177
            L LIYV+LG+GLNIVVGLAGLLDLGYV FYA+GAY  AL  +Y G GFW+ LP+A + A
Sbjct: 132 ILGLIYVLLGLGLNIVVGLAGLLDLGYVAFYAIGAYGLALGYQYLGLGFWSVLPLAAIAA 191

Query: 178 ALFGFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNMTEITGGPNGIGSIPKPTLFGLTF 237
           AL G +LGFPVLR+ GDYLAIVTLGFGEIIR++L N    TGGPNG+ + P PT FGL F
Sbjct: 192 ALAGCILGFPVLRMHGDYLAIVTLGFGEIIRLVLNNWLSFTGGPNGMPA-PSPTFFGLEF 250

Query: 238 ERRAPEGMQTFHEFFGIAYNTNYKVILLYVVALLLVLLALFVINRLMRMPIGRAWEALRE 297
            RRA +G    HEFFG  YN + K + +Y V  ++VL  L++ +RL RMP+GRAWEALRE
Sbjct: 251 GRRAKDGGVPIHEFFGFEYNASLKFVFIYAVLFMVVLAVLYIKHRLTRMPVGRAWEALRE 310

Query: 298 DEVACRALGLNPTIVKLSAFTIGASFAGFAGSFFAARQGLVTPESFTFIESAMILAIVVL 357
           DE+ACR++GLN  +VKLSAFT+GAS AG AG FFA  QG V P SFTF ESA+ILAIVVL
Sbjct: 311 DEIACRSMGLNHVLVKLSAFTLGASTAGLAGVFFATYQGFVNPSSFTFFESALILAIVVL 370

Query: 358 GGMGSQLGVILAAVVMVLLQE-MRGFNEYRMLIFGLTMIVMMIWRPQGLLPMQR 410
           GGMGS +GV++AA V+ +  E +R F+EYR+L+FG+ M++MMIWRP+GL+ + R
Sbjct: 371 GGMGSTVGVVIAAFVLTVAPELLRSFSEYRVLLFGVLMVLMMIWRPRGLIRISR 424


Lambda     K      H
   0.330    0.146    0.439 

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: 633
Number of extensions: 36
Number of successful extensions: 3
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: 417
Length of database: 435
Length adjustment: 32
Effective length of query: 385
Effective length of database: 403
Effective search space:   155155
Effective search space used:   155155
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 51 (24.3 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