GapMind for catabolism of small carbon sources

 

Aligments for a candidate for AZOBR_RS08235 in Pseudomonas stutzeri RCH2

Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate GFF1278 Psest_1311 Branched-chain amino acid ABC-type transport system, permease components

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



>lcl|FitnessBrowser__psRCH2:GFF1278 Psest_1311 Branched-chain amino
           acid ABC-type transport system, permease components
          Length = 307

 Score =  362 bits (929), Expect = e-105
 Identities = 174/302 (57%), Positives = 240/302 (79%), Gaps = 3/302 (0%)

Query: 3   YFLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSLGI 62
           ++LQQLINGL++G+ Y LIAIGYTMVYGIIGMINFAHGE+YMIG++V  I  + +  +G+
Sbjct: 6   HYLQQLINGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVTFIAIVGLSMMGL 65

Query: 63  TWVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQILQ 122
             +P+ ++   VA+M+ T+ YG+++ER+AYRPLR S RL PLISAIGMSIFLQN V + Q
Sbjct: 66  DALPILMIGAFVAAMIVTSAYGYSIERVAYRPLRGSNRLIPLISAIGMSIFLQNVVLLAQ 125

Query: 123 GARSKPLQPILPGNLTLMDGAVS---VSYVRLATIVITIALMYGFTQLITRTSLGRAQRA 179
            ++ K +  ++PGNL + + A++   +SY+++   V+T   MYG T  I+R+ LGRA RA
Sbjct: 126 DSKDKAIPNLMPGNLVIGESAMNGVVISYMQILIFVVTFVAMYGLTLFISRSRLGRACRA 185

Query: 180 CEQDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAA 239
           C +D KMA LLG+N + +I+LTFV+GAALAAVA +++ + YGVI+ +IGFLAG+KAFTAA
Sbjct: 186 CAEDLKMANLLGINTNSIIALTFVIGAALAAVAAVLISMQYGVINPHIGFLAGIKAFTAA 245

Query: 240 VLGGIGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGLLGRPEIE 299
           VLGGIGS+PGAMLGG+V+G+ EAF +   G ++KDV  F++L+LVL+FRPTG+LGRPE+E
Sbjct: 246 VLGGIGSIPGAMLGGLVLGVAEAFGADIFGDQYKDVVAFSLLILVLLFRPTGILGRPEVE 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: 417
Number of extensions: 13
Number of successful extensions: 3
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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