GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08235 in Pseudomonas fluorescens FW300-N2E3

Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate AO353_17120 AO353_17120 branched-chain amino acid transporter permease subunit LivH

Query= reanno::azobra:AZOBR_RS08235
         (301 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_17120
          Length = 307

 Score =  345 bits (884), Expect = e-99
 Identities = 172/302 (56%), Positives = 231/302 (76%), Gaps = 3/302 (0%)

Query: 3   YFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSLGI 62
           +F QQL+NGL++G+ Y LIAIGYTMVYGIIGMINFAHGE+YMIG++VA I    +  LGI
Sbjct: 6   HFFQQLVNGLTIGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVAFIVLAGLAMLGI 65

Query: 63  TWVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQILQ 122
             +PL +    +A+++ T+ YG+++ERIAYRPLR S RL PLISAIGMSIFLQN V + Q
Sbjct: 66  HSLPLLMTAAFLATIVVTSAYGYSIERIAYRPLRGSNRLIPLISAIGMSIFLQNTVLLSQ 125

Query: 123 GARSKPLQPILPGNLTLMDGA---VSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRA 179
            ++ K +  ++PG+ +   G    V +SY+++   V+T+ +M   T  I+R+ LGRA RA
Sbjct: 126 DSKDKSIPNLIPGSFSFGPGGAQEVLISYMQILVFVVTLVVMLCLTTFISRSRLGRACRA 185

Query: 180 CEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAA 239
           C +D +MA LLG+N + +I+LTFV+GAALAAVA +++ + YGVI+   GFL G+KAFTAA
Sbjct: 186 CAEDIRMANLLGINTNNIIALTFVIGAALAAVAAVLLSMQYGVINPNAGFLVGLKAFTAA 245

Query: 240 VLGGIGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGLLGRPEIE 299
           VLGGIGS+PGAMLGG+V+G+ EAF +   G ++KDV  F +LVLVL+FRPTGLLGRPE+E
Sbjct: 246 VLGGIGSIPGAMLGGLVLGVAEAFGADIFGDQYKDVVAFGLLVLVLLFRPTGLLGRPEVE 305

Query: 300 KV 301
           KV
Sbjct: 306 KV 307


Lambda     K      H
   0.329    0.144    0.425 

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: 386
Number of extensions: 11
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: 301
Length of database: 307
Length adjustment: 27
Effective length of query: 274
Effective length of database: 280
Effective search space:    76720
Effective search space used:    76720
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.

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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