GapMind for catabolism of small carbon sources

 

Aligments for a candidate for SMc02873 in Phaeobacter inhibens BS107

Align N-Acetyl-D-glucosamine ABC transport system, periplasmic substrate-binding component (characterized)
to candidate GFF2750 PGA1_c27930 putative sugar ABC transporter, periplasmic binding protein

Query= reanno::Phaeo:GFF2750
         (417 letters)



>lcl|FitnessBrowser__Phaeo:GFF2750 PGA1_c27930 putative sugar ABC
           transporter, periplasmic binding protein
          Length = 417

 Score =  850 bits (2197), Expect = 0.0
 Identities = 417/417 (100%), Positives = 417/417 (100%)

Query: 1   MTRKLFTLALLGSTMIGGAAAAEDVTLTIESWRNDDLALWQDKIIPAFEAANPGIKLKFT 60
           MTRKLFTLALLGSTMIGGAAAAEDVTLTIESWRNDDLALWQDKIIPAFEAANPGIKLKFT
Sbjct: 1   MTRKLFTLALLGSTMIGGAAAAEDVTLTIESWRNDDLALWQDKIIPAFEAANPGIKLKFT 60

Query: 61  PSAPAEYNAVLNSKLDAGSAGDLITCRPFDASLGLYDKGQLADLSDLDAMGSFSNVAKSA 120
           PSAPAEYNAVLNSKLDAGSAGDLITCRPFDASLGLYDKGQLADLSDLDAMGSFSNVAKSA
Sbjct: 61  PSAPAEYNAVLNSKLDAGSAGDLITCRPFDASLGLYDKGQLADLSDLDAMGSFSNVAKSA 120

Query: 121 WQTDDGSATFCVPIASVIHGFIYNKDAFAELGVNVPETEDEFFAALEKIKEDGNYVPLAM 180
           WQTDDGSATFCVPIASVIHGFIYNKDAFAELGVNVPETEDEFFAALEKIKEDGNYVPLAM
Sbjct: 121 WQTDDGSATFCVPIASVIHGFIYNKDAFAELGVNVPETEDEFFAALEKIKEDGNYVPLAM 180

Query: 181 GTNDQWEAATMGYNNIGPNYWKGEEGRLALIAGEQKLTDDQWVAPYETLSKWGAYMGDGY 240
           GTNDQWEAATMGYNNIGPNYWKGEEGRLALIAGEQKLTDDQWVAPYETLSKWGAYMGDGY
Sbjct: 181 GTNDQWEAATMGYNNIGPNYWKGEEGRLALIAGEQKLTDDQWVAPYETLSKWGAYMGDGY 240

Query: 241 EAQTYPDSQNIFTLGRAAIYPAGSWEISGFNTQADFAMGAFKPPVKAAGDTCYISDHTDI 300
           EAQTYPDSQNIFTLGRAAIYPAGSWEISGFNTQADFAMGAFKPPVKAAGDTCYISDHTDI
Sbjct: 241 EAQTYPDSQNIFTLGRAAIYPAGSWEISGFNTQADFAMGAFKPPVKAAGDTCYISDHTDI 300

Query: 301 AVGLNAASPNAEAAKTFLNWVGSAEFASIYANALPGFFSLSNHEVAMEDPLAQEFVSWRG 360
           AVGLNAASPNAEAAKTFLNWVGSAEFASIYANALPGFFSLSNHEVAMEDPLAQEFVSWRG
Sbjct: 301 AVGLNAASPNAEAAKTFLNWVGSAEFASIYANALPGFFSLSNHEVAMEDPLAQEFVSWRG 360

Query: 361 ECESTIRSTYQILSRGTPNLENETWGASVAAIKGTKAPADLGAELQEGLASWYEPQK 417
           ECESTIRSTYQILSRGTPNLENETWGASVAAIKGTKAPADLGAELQEGLASWYEPQK
Sbjct: 361 ECESTIRSTYQILSRGTPNLENETWGASVAAIKGTKAPADLGAELQEGLASWYEPQK 417


Lambda     K      H
   0.314    0.131    0.399 

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: 925
Number of extensions: 29
Number of successful extensions: 1
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: 417
Length of database: 417
Length adjustment: 31
Effective length of query: 386
Effective length of database: 386
Effective search space:   148996
Effective search space used:   148996
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 50 (23.9 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