GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Pf6N2E2_5404 in Pseudomonas simiae WCS417

Align ABC transporter for D-Alanine, permease component 1 (characterized)
to candidate GFF968 PS417_04910 amino acid ABC transporter permease

Query= reanno::pseudo6_N2E2:Pf6N2E2_5404
         (365 letters)



>FitnessBrowser__WCS417:GFF968
          Length = 365

 Score =  682 bits (1759), Expect = 0.0
 Identities = 329/365 (90%), Positives = 347/365 (95%)

Query: 1   MTTHTFKPDMPPPGSSIGVVAWMRANMFSSWINTLLTLFAFYLIYLIVPPLVQWAILDAN 60
           M++HTFKPDMPPP    G +AWMRAN+FSSW+NTLLTL AFYLIYL+VPP++ WAI+DAN
Sbjct: 1   MSSHTFKPDMPPPNKVFGPMAWMRANLFSSWLNTLLTLLAFYLIYLVVPPILSWAIIDAN 60

Query: 61  WVGTTRADCTKEGACWVFIQQRFGQFMYGYYPADLRWRVDLTVWLAVIGVAPLFISRFPR 120
           WVGTTRADCTKEGACWVFIQQRFGQFMYGYYP DLRWRVDLTVWLA++GVAPLFISRF R
Sbjct: 61  WVGTTRADCTKEGACWVFIQQRFGQFMYGYYPGDLRWRVDLTVWLAIVGVAPLFISRFQR 120

Query: 121 KAIYGLSFLVLYPISAWCLLHGGVFGLDAVATSQWGGLMLTLVIATVGIVGALPLGIVLA 180
           KA+YGL FLVLYPI A+ LLHGG+FGL  VATSQWGGLMLTLVIATVGI GALPLGI+LA
Sbjct: 121 KAVYGLGFLVLYPIIAFFLLHGGIFGLTNVATSQWGGLMLTLVIATVGIAGALPLGIMLA 180

Query: 181 LGRRSNMPAIRVVCVTFIEFWRGVPLITVLFMSSVMLPLFLPEGMNFDKLLRALIGVILF 240
           LGRRSNMPAIRVVCVTFIEFWRGVPLITVLFMSSVMLPLFLPEGM  DKLLRALIGVILF
Sbjct: 181 LGRRSNMPAIRVVCVTFIEFWRGVPLITVLFMSSVMLPLFLPEGMGIDKLLRALIGVILF 240

Query: 241 QSAYIAEVVRGGLQAIPKGQYEAAAAMGLGYWRSMGLVILPQALKLVIPGIVNTFIALFK 300
           QSAY+AEVVRGGLQAIPKGQYEAAAAMGLGYWRSMGLVILPQALK+VIPGIVNTFIALFK
Sbjct: 241 QSAYVAEVVRGGLQAIPKGQYEAAAAMGLGYWRSMGLVILPQALKMVIPGIVNTFIALFK 300

Query: 301 DTSLVIIIGLFDLLNSVKQAAADPKWLGMATEGYVFAALVFWIFCFGMSRYSMHLERKLD 360
           DTSLVIIIGLFDLLNSVKQAAADPKWLGMATEGYVFAALVFWIFCFGMSRYS+HLE KLD
Sbjct: 301 DTSLVIIIGLFDLLNSVKQAAADPKWLGMATEGYVFAALVFWIFCFGMSRYSIHLEHKLD 360

Query: 361 TGHKR 365
           TGHKR
Sbjct: 361 TGHKR 365


Lambda     K      H
   0.330    0.144    0.469 

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: 774
Number of extensions: 31
Number of successful extensions: 1
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: 365
Length of database: 365
Length adjustment: 30
Effective length of query: 335
Effective length of database: 335
Effective search space:   112225
Effective search space used:   112225
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 (21.9 bits)
S2: 49 (23.5 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