GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Pseudomonas simiae WCS417

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate GFF1301 PS417_06610 branched-chain amino acid transporter permease subunit LivH

Query= uniprot:Q1MCU0
         (300 letters)



>FitnessBrowser__WCS417:GFF1301
          Length = 307

 Score =  299 bits (766), Expect = 5e-86
 Identities = 157/304 (51%), Positives = 214/304 (70%), Gaps = 8/304 (2%)

Query: 3   YFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI-F 61
           +F QQL+NGLT+GS Y L+AIGYTMVYGIIGMINFAHG+++M+G + A I    L  +  
Sbjct: 6   HFFQQLVNGLTIGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVAFIALAGLAMMGI 65

Query: 62  AGLPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQV 121
             LP+  L+    + ++++TS + ++IERVAYRPLRGS RL PLI+AIGMSI L N + +
Sbjct: 66  HSLPL--LMTAAFLASIVVTSAYGYSIERVAYRPLRGSNRLIPLISAIGMSIFLQNTVLL 123

Query: 122 TQGPRNKPIPPMVSSVYQFG-----NISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQ 176
           +Q  ++K IP ++   + FG      + +S  QI++ V+T V +      ++R+ LGRA 
Sbjct: 124 SQDSKDKSIPNLIPGSFSFGPGGAEEVLISYMQILVFVVTLVAMLGLTLFISRSRLGRAC 183

Query: 177 RATEQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFT 236
           RA  +D KMA LLG+N +  I++TFV+GAALAAVA  +  M YGV + N GF  G+KAFT
Sbjct: 184 RACAEDIKMANLLGINTNNIIALTFVIGAALAAVAAVLLSMQYGVINPNAGFLVGLKAFT 243

Query: 237 AAVLGGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILGRPE 296
           AAVLGGIGS+PGA+ GGL++G+ E+  +  F   YKDV  F +L  VL+F+PTGILGRPE
Sbjct: 244 AAVLGGIGSIPGAMLGGLVLGVAEAFGADIFGDQYKDVVAFGLLVLVLLFRPTGILGRPE 303

Query: 297 VEKV 300
           VEKV
Sbjct: 304 VEKV 307


Lambda     K      H
   0.329    0.143    0.421 

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: 355
Number of extensions: 12
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: 300
Length of database: 307
Length adjustment: 27
Effective length of query: 273
Effective length of database: 280
Effective search space:    76440
Effective search space used:    76440
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: 48 (23.1 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