GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livM in Pseudomonas simiae WCS417

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 GFF523 PS417_02665 branched-chain amino acid ABC transporter permease

Query= TCDB::P21628
         (417 letters)



>FitnessBrowser__WCS417:GFF523
          Length = 425

 Score =  417 bits (1072), Expect = e-121
 Identities = 222/416 (53%), Positives = 290/416 (69%), Gaps = 16/416 (3%)

Query: 1   MSQSLKRALFSALLVILVSYPILGLKLRTVGIKLEVLGADAQTLWTIAAAALAMFVWQLF 60
           + +S+   + + L+ ++V  PI+G+ L      LE     A+    +A   +  F   LF
Sbjct: 9   IKKSVVDTVLAGLISLVVFGPIVGVVLDGYSFNLE----PARVALLVAIVMVGRFAMSLF 64

Query: 61  RDRIPLKLGRGV----GYKVNGSGLKNFL-SLPSTQRWAVLALVVVAFVWPFFASRGAVD 115
                L+  +GV    G++  GSG+        S  RW + AL+V+A V+P FA++  + 
Sbjct: 65  -----LQTPKGVKILQGFESTGSGVHVLAPDYKSRLRWIIPALIVIAIVFPIFANKYLLT 119

Query: 116 IATLILIYVMLGIGLNIVVGLAGLLDLGYVGFYAVGAYTYALLAEYAGFGFWTALPIAGM 175
           +  L LIYV+LG+GLNIVVGLAGLLDLGYV FYA+GAY  AL  +Y G GFWT LP+A +
Sbjct: 120 VVILGLIYVLLGLGLNIVVGLAGLLDLGYVAFYAIGAYGLALGYQYLGLGFWTVLPLAAI 179

Query: 176 MAALFGFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNMTEITGGPNGIGSIPKPTLFGL 235
            AAL G +LGFPVLR+ GDYLAIVTLGFGEIIR++L N    TGGPNG+  +P PT  GL
Sbjct: 180 AAALAGCILGFPVLRMHGDYLAIVTLGFGEIIRLVLNNWLSFTGGPNGM-PVPSPTFLGL 238

Query: 236 TFERRAPEGMQTFHEFFGIAYNTNYKVILLYVVALLLVLLALFVINRLMRMPIGRAWEAL 295
            F +RA +G   FHEFFGI YN N K + +Y+V  L+VL  L++ +RL RMP+GRAWEAL
Sbjct: 239 EFGKRAKDGGIPFHEFFGIDYNPNIKFLFIYIVLFLVVLAVLYIKHRLTRMPVGRAWEAL 298

Query: 296 REDEVACRALGLNPTIVKLSAFTIGASFAGFAGSFFAARQGLVTPESFTFIESAMILAIV 355
           REDE+ACR++GLN  +VKLSAFTIGAS AG AG FFA+ QG V P SFTF ESA+ILAIV
Sbjct: 299 REDEIACRSMGLNHVLVKLSAFTIGASTAGLAGVFFASYQGFVNPSSFTFFESALILAIV 358

Query: 356 VLGGMGSQLGVILAAVVMVLLQE-MRGFNEYRMLIFGLTMIVMMIWRPQGLLPMQR 410
           VLGGMGS +GV++AA V+ +  E +R F+EYR+L+FG+ M+VMMIWRP+GL+ + R
Sbjct: 359 VLGGMGSTVGVVIAAFVLTVAPELLRSFSEYRVLLFGVLMVVMMIWRPRGLIRISR 414


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: 618
Number of extensions: 39
Number of successful extensions: 4
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: 425
Length adjustment: 32
Effective length of query: 385
Effective length of database: 393
Effective search space:   151305
Effective search space used:   151305
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.

Links

Downloads

Related tools

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