GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livM in Pseudomonas fluorescens FW300-N2C3

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 AO356_08490 AO356_08490 branched-chain amino acid ABC transporter permease

Query= TCDB::P21628
         (417 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_08490
          Length = 426

 Score =  425 bits (1093), Expect = e-123
 Identities = 224/412 (54%), Positives = 291/412 (70%), Gaps = 8/412 (1%)

Query: 1   MSQSLKRALFSALLVILVSYPILGLKLRTVGIKLEVLGADAQTLWTIAAAALAMFVWQLF 60
           + QS+  A+ + L+ ++V  PI+G+ L      L+     A+  W +A   +  F   LF
Sbjct: 10  IKQSVIDAILAGLISLIVFGPIVGVVLDGYSFNLQ----PARVGWLVAIVMIGRFALSLF 65

Query: 61  RDRIPLKLGRGVGYKVNGSGLKNFL-SLPSTQRWAVLALVVVAFVWPFFASRGAVDIATL 119
             + P  L    G++  GSG+        S  RW + AL+V+A V+PFFA++  + +  L
Sbjct: 66  L-QTPKGLKILQGFESTGSGVHVLPPDYKSRLRWIIPALIVIAIVFPFFANKYVLTVVIL 124

Query: 120 ILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYTYALLAEYAGFGFWTALPIAGMMAAL 179
            LIYV+LG+GLNIVVGLAGLLDLGYV FYA+GAY  AL  +Y G GFWT LP+A + AA+
Sbjct: 125 GLIYVLLGLGLNIVVGLAGLLDLGYVAFYAIGAYGLALGYQYLGLGFWTVLPLAAIAAAM 184

Query: 180 FGFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNMTEITGGPNGIGSIPKPTLFGLTFER 239
            G +LGFPVLR+ GDYLAIVTLGFGEIIR++L N    TGGPNG+  +P PT  GL F R
Sbjct: 185 AGCILGFPVLRMHGDYLAIVTLGFGEIIRLVLNNWLSFTGGPNGM-PVPSPTFLGLEFGR 243

Query: 240 RAPEGMQTFHEFFGIAYNTNYKVILLYVVALLLVLLALFVINRLMRMPIGRAWEALREDE 299
           RA +G   FHEFFGI YN N K + +Y+V  + VLL L+V +RL RMP+GRAWEALREDE
Sbjct: 244 RAKDGGVPFHEFFGIDYNPNIKFLFIYIVLFITVLLVLYVKHRLTRMPVGRAWEALREDE 303

Query: 300 VACRALGLNPTIVKLSAFTIGASFAGFAGSFFAARQGLVTPESFTFIESAMILAIVVLGG 359
           +ACR++GLN  +VKLSAFTIGAS AG AG FFA+ QG V P SFTF ESA+ILAIVVLGG
Sbjct: 304 IACRSMGLNHVLVKLSAFTIGASTAGLAGVFFASYQGFVNPSSFTFFESALILAIVVLGG 363

Query: 360 MGSQLGVILAAVVMVLLQE-MRGFNEYRMLIFGLTMIVMMIWRPQGLLPMQR 410
           MGS +GV++AA V+ +  E +R F+EYR+L+FG+ M++MMIWRP+GL+ + R
Sbjct: 364 MGSTVGVVIAAFVLTVAPELLRSFSEYRVLLFGVLMVLMMIWRPRGLIRISR 415


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: 614
Number of extensions: 38
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: 417
Length of database: 426
Length adjustment: 32
Effective length of query: 385
Effective length of database: 394
Effective search space:   151690
Effective search space used:   151690
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