GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03050 in Pseudomonas fluorescens FW300-N2C3

Align ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized)
to candidate AO356_27115 AO356_27115 amino acid ABC transporter permease

Query= reanno::pseudo3_N2E3:AO353_03050
         (229 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_27115
          Length = 242

 Score =  237 bits (604), Expect = 2e-67
 Identities = 117/226 (51%), Positives = 167/226 (73%), Gaps = 1/226 (0%)

Query: 2   LKGYGAVILDGAWLTLQLALSSMALAIVLGLIGVALRLSPIRWLARLGDLYSTVIRGIPD 61
           L+G+G ++L+GAW+T++L+LS++AL+++LGLIG + +LS ++ L     LY+T+IRG+PD
Sbjct: 16  LQGFGPLLLEGAWMTVKLSLSALALSVLLGLIGASAKLSSLKLLRLPAQLYTTLIRGVPD 75

Query: 62  LVLILLIFYGGQDLLNRVAPLLGYDDYIDLNPLVAGIGTLGFIFGAYLSETFRGAFMAIP 121
           LVL+LLIFY  Q  L  +   LG++ YI++NP VAGI TLGFI+GAY +ETFRGA +A+P
Sbjct: 76  LVLMLLIFYSLQTWLTVITVALGWE-YIEINPFVAGIITLGFIYGAYFTETFRGAMLAVP 134

Query: 122 KGQAEAGAAYGMSSFQVFFRVLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFKA 181
           +GQ EA  AYG+S  Q F  V+ PQM+R A+PG  NNW+V+ KATAL+S++GL D++  A
Sbjct: 135 RGQVEAATAYGLSRAQRFRFVVFPQMMRFALPGLGNNWMVILKATALVSIIGLADLVKAA 194

Query: 182 KQAADATREPFTFFLAVAAMYLVITSVSLLALRHLEKRYSVGVRAA 227
           + A  +T + F F +  A  YL+ITS+S   LR LEK Y+ G R A
Sbjct: 195 QDAGKSTYQLFFFLVLAALTYLIITSISNFVLRCLEKHYAAGSREA 240


Lambda     K      H
   0.329    0.144    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: 207
Number of extensions: 10
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: 242
Length adjustment: 23
Effective length of query: 206
Effective length of database: 219
Effective search space:    45114
Effective search space used:    45114
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