GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livM 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_1139 PP_1139 branched chain amino acid transporter - permease subunit

Query= TCDB::P21628
         (417 letters)



>FitnessBrowser__Putida:PP_1139
          Length = 418

 Score =  600 bits (1547), Expect = e-176
 Identities = 304/417 (72%), Positives = 354/417 (84%), Gaps = 1/417 (0%)

Query: 1   MSQSLKRALFSALLVILVSYPILGLKLRTVGIKLEVLGADAQTLWTIAAAALAMFVWQLF 60
           M+++LK+A FSALLV  V++P+LGLKL   GI L V    + T+  IA  ++ MF+  LF
Sbjct: 1   MNRNLKQAFFSALLVWAVAFPVLGLKLSIDGISLVVHSQGSFTISIIAVCSVLMFLRVLF 60

Query: 61  RDRIPLKLGRGVGYKVNGSGLKNFLSLPSTQRWAVLALVVVAFVWPFFASRGAVDIATLI 120
             +    +GR    K+    + N+L+LP TQR+ ++ L+VVA VWPFF SRGAVDIATLI
Sbjct: 61  DKQWSSVMGRRSDRKLIPPAVSNYLTLPKTQRYVIIGLIVVALVWPFFGSRGAVDIATLI 120

Query: 121 LIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYTYALLAEYAGFGFWTALPIAGMMAALF 180
           LIYV+LG+GLNIVVGLAGLLDLGYVGFYAVGAY+YA+L+ Y G+ FW  LPIAG+MAA F
Sbjct: 121 LIYVLLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYAMLSHYLGWSFWVCLPIAGLMAATF 180

Query: 181 GFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNMTEITGGPNGIGSIPKPTLFGLTFERR 240
           GFLLGFPVLRLRGDYLAIVTLGFGEIIR+ LRN+T+ TGGPNGI +IPKP  FGLTFERR
Sbjct: 181 GFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDWTGGPNGISNIPKPEFFGLTFERR 240

Query: 241 APEGMQTFHEFFGIAYNTNYKVILLYVVALLLVLLALFVINRLMRMPIGRAWEALREDEV 300
           A EGMQTFHEFFG+ YN+  KVI LY+VALLL LLALFVINRL+RMPIGRAWEALREDE+
Sbjct: 241 AAEGMQTFHEFFGLQYNSINKVIFLYLVALLLALLALFVINRLLRMPIGRAWEALREDEI 300

Query: 301 ACRALGLNPTIVKLSAFTIGASFAGFAGSFFAARQGLVTPESFTFIESAMILAIVVLGGM 360
           ACRALGLNPT++KLSAFT+GA FAGFAGSFFAARQGLVTPESFTFIESA+ILAIVVLGGM
Sbjct: 301 ACRALGLNPTVIKLSAFTLGACFAGFAGSFFAARQGLVTPESFTFIESAIILAIVVLGGM 360

Query: 361 GSQLGVILAAVVMVLLQE-MRGFNEYRMLIFGLTMIVMMIWRPQGLLPMQRPHLELK 416
           GSQLGVILAA+VM+LL E MR F+EYRML+FG  M++MMIWRPQGLLPMQRPH+EL+
Sbjct: 361 GSQLGVILAAIVMILLPELMREFSEYRMLMFGALMVLMMIWRPQGLLPMQRPHMELR 417


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: 646
Number of extensions: 29
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: 417
Length of database: 418
Length adjustment: 32
Effective length of query: 385
Effective length of database: 386
Effective search space:   148610
Effective search space used:   148610
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: 50 (23.9 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