GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03050 in Pseudomonas stutzeri RCH2

Align ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized)
to candidate GFF137 Psest_0137 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family

Query= reanno::pseudo1_N1B4:Pf1N1B4_3432
         (229 letters)



>FitnessBrowser__psRCH2:GFF137
          Length = 231

 Score =  217 bits (552), Expect = 2e-61
 Identities = 105/227 (46%), Positives = 161/227 (70%), Gaps = 2/227 (0%)

Query: 2   LKGYGAVILDGVWLTLQLALSSMVLAIVLGLIGVALRLSPIRWLAWLGDLYSTVIRGIPD 61
           L G+G  ++ G W+T+QLAL+S+ L +VLGL+G   + SP   L WLG  YST++RG+P+
Sbjct: 5   LHGFGPALIAGTWMTIQLALASLALGLVLGLLGALAKTSPYSALRWLGGTYSTIVRGVPE 64

Query: 62  LVLILLIFYGGQDLLNRVAPMFGYDDYIDLNPLAAGIGTLGFIFGAYLSETFRGAFMAIP 121
           L+ +LLI++G   ++  +  +FG ++ + L+P AAG   LG  FGAY +E FRGA +AIP
Sbjct: 65  LLWVLLIYFGTISMIRGIGELFGIEN-LALSPFAAGTIALGLCFGAYATEVFRGALLAIP 123

Query: 122 KGQAEAGMAYGMSSFQVFFRVLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFKA 181
           KG  EAG+A G+   ++F R+++PQM RLA+PG  N +++L K TAL+SV+GL+++M ++
Sbjct: 124 KGHREAGLALGLGKRRIFTRLILPQMWRLALPGLGNLFMILMKDTALVSVIGLEEIMRRS 183

Query: 182 KQAADATREPFTFFLAVAAMYLVITSVSLLALRHLEKRYSVG-VRAA 227
           + A  A++EPFTFFL  A +YL +T V+++ +  LEKR   G VR+A
Sbjct: 184 QIAVTASKEPFTFFLVAAFIYLCLTIVAMVGMHFLEKRAGRGFVRSA 230


Lambda     K      H
   0.329    0.144    0.428 

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: 212
Number of extensions: 9
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: 229
Length of database: 231
Length adjustment: 23
Effective length of query: 206
Effective length of database: 208
Effective search space:    42848
Effective search space used:    42848
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: 46 (22.3 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