GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natH in Pseudomonas simiae WCS417

Align Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale)
to candidate GFF968 PS417_04910 amino acid ABC transporter permease

Query= uniprot:Q31RN9
         (396 letters)



>FitnessBrowser__WCS417:GFF968
          Length = 365

 Score =  254 bits (650), Expect = 2e-72
 Identities = 148/398 (37%), Positives = 225/398 (56%), Gaps = 76/398 (19%)

Query: 14  PIAWLRQNLFSSWLNSAITLLLVVIIVTVVGRLGLWITTEARWT---------------V 58
           P+AW+R NLFSSWLN+ +TLL   +I  VV  +  W   +A W                 
Sbjct: 19  PMAWMRANLFSSWLNTLLTLLAFYLIYLVVPPILSWAIIDANWVGTTRADCTKEGACWVF 78

Query: 59  LVDNWTLFFVGRYPAAEQWR--LWLWLGLLSPTLGLTWGCLATGSHRWQRRSLWGWAGLA 116
           +   +  F  G YP   +WR  L +WL ++        G       R+QR++++G     
Sbjct: 79  IQQRFGQFMYGYYPGDLRWRVDLTVWLAIV--------GVAPLFISRFQRKAVYG----- 125

Query: 117 AAIAGIPLPWFPHKLGLAAIAATVPAASWLAQRCRGQAWLRFLPTLWGVLF-LVGLWLLQ 175
                                                  L FL     VL+ ++  +LL 
Sbjct: 126 ---------------------------------------LGFL-----VLYPIIAFFLLH 141

Query: 176 GGL-GLRPVSSNDWSGLLLTLATALISMVCSLPLGILLALGRQSSLPAIRWLSVTYIELF 234
           GG+ GL  V+++ W GL+LTL  A + +  +LPLGI+LALGR+S++PAIR + VT+IE +
Sbjct: 142 GGIFGLTNVATSQWGGLMLTLVIATVGIAGALPLGIMLALGRRSNMPAIRVVCVTFIEFW 201

Query: 235 RGLPLVTILFFGQVMVPLMLDSEWRIDRILRAIVGLTIFLSAYLAETVRGGLQAIPQGQF 294
           RG+PL+T+LF   VM+PL L     ID++LRA++G+ +F SAY+AE VRGGLQAIP+GQ+
Sbjct: 202 RGVPLITVLFMSSVMLPLFLPEGMGIDKLLRALIGVILFQSAYVAEVVRGGLQAIPKGQY 261

Query: 295 EAAAALGLNLFQTYRFIVLPQALRISIPAIVGLFLNLLQDTTLLSIVGLLELLGISRSIL 354
           EAAAA+GL  +++   ++LPQAL++ IP IV  F+ L +DT+L+ I+GL +LL   +   
Sbjct: 262 EAAAAMGLGYWRSMGLVILPQALKMVIPGIVNTFIALFKDTSLVIIIGLFDLLNSVKQAA 321

Query: 355 ANPAYLGRYAEVYLFLGVLYWLCCYGLAQLSRRLEQRL 392
           A+P +LG   E Y+F  +++W+ C+G+++ S  LE +L
Sbjct: 322 ADPKWLGMATEGYVFAALVFWIFCFGMSRYSIHLEHKL 359


Lambda     K      H
   0.329    0.142    0.471 

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: 443
Number of extensions: 15
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 396
Length of database: 365
Length adjustment: 30
Effective length of query: 366
Effective length of database: 335
Effective search space:   122610
Effective search space used:   122610
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 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