GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutX in Pseudomonas fluorescens FW300-N2E2

Align HutX aka HISX, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate Pf6N2E2_530 Histidine transporter, periplasmic histidine-binding protein

Query= TCDB::Q9KKE3
         (346 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_530
          Length = 336

 Score =  312 bits (800), Expect = 7e-90
 Identities = 145/309 (46%), Positives = 205/309 (66%), Gaps = 2/309 (0%)

Query: 37  VTFAGIDWESGAFITEVMKTILSKGYDCQVDSIPGNSVTLEQATANNDVQIFAEEWLGRS 96
           + FA ++WESG+ IT++++ I+ KGY  Q D++PG ++TLE A ANND+Q+  EEW GRS
Sbjct: 30  IHFADLNWESGSLITDILRIIVEKGYGLQTDTLPGTTITLETALANNDIQVIGEEWAGRS 89

Query: 97  DVWNKAVEEKKVIAVGKTFVGASEGWFVPDYVVHGDPARNIEAKAPDLKSVSQLTDPKIA 156
            VW KA  E KV+A+G T  GA+EGW+VP+YV+ GDPA+ I+  APDL+SV  L   K  
Sbjct: 90  PVWVKAEAEGKVVALGDTVKGATEGWWVPEYVIKGDPAKGIKPLAPDLRSVEDLARYK-- 147

Query: 157 EIFADPEEPSKGRFLNCPSGWTCEGVSTAKLEAYKLGETYVNFRPGTGTALDAAITSAYL 216
            +F DPE P KGRFLN P GWT E V+  KL+AY L ++YVNFR G+G ALDA I+S   
Sbjct: 148 HVFKDPESPDKGRFLNSPIGWTSEVVNKQKLKAYGLSDSYVNFRSGSGAALDAEISSTIR 207

Query: 217 QGEPIFFYYWSPTAILGKFKLIQLEEPAYNEACWKELSSANGKRDEGCAFPSVDVAYGVN 276
           +G+PI FYYWSPT +LG+FKL+QL+EP ++   WK L+ A+    +     +  ++ GV+
Sbjct: 208 RGKPILFYYWSPTPLLGRFKLVQLQEPPFDAEAWKTLTDADNPNPKPTRSLASKLSIGVS 267

Query: 277 STFASEAPEIVEILEKATFPLDEVNASLAYMADNKVDATAAAAEFLKTKGDIWSKWVSDE 336
           + F  + P+I E   K   P++ +N +LA M++ ++    AA  FLK    +W  W+  E
Sbjct: 268 APFQKQYPDIAEFFSKVDLPIEPLNKALADMSEKRIPPREAAEAFLKAHPQVWQAWLPKE 327

Query: 337 ARGKIEAGL 345
              K+ AGL
Sbjct: 328 VADKVSAGL 336


Lambda     K      H
   0.314    0.130    0.391 

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: 352
Number of extensions: 13
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: 346
Length of database: 336
Length adjustment: 29
Effective length of query: 317
Effective length of database: 307
Effective search space:    97319
Effective search space used:    97319
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 49 (23.5 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