GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livH in Pseudomonas fluorescens FW300-N2E3

Align High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate AO353_17120 AO353_17120 branched-chain amino acid transporter permease subunit LivH

Query= TCDB::P21627
         (307 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_17120 AO353_17120
           branched-chain amino acid transporter permease subunit
           LivH
          Length = 307

 Score =  506 bits (1302), Expect = e-148
 Identities = 253/307 (82%), Positives = 281/307 (91%)

Query: 1   MPEIYHYLQQLVNGLTVGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYIAFIAITLL 60
           MPEIYH+ QQLVNGLT+GSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSY+AFI +  L
Sbjct: 1   MPEIYHFFQQLVNGLTIGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVAFIVLAGL 60

Query: 61  AMMGLDSVPLMMLAAFAASIIVTSAFGYSIERVAYRPLRGGNRLIPLISAIGMSIFLQNA 120
           AM+G+ S+PL+M AAF A+I+VTSA+GYSIER+AYRPLRG NRLIPLISAIGMSIFLQN 
Sbjct: 61  AMLGIHSLPLLMTAAFLATIVVTSAYGYSIERIAYRPLRGSNRLIPLISAIGMSIFLQNT 120

Query: 121 VMLSQDSKEKAIPTLLPGNFVFGESSMNGVVISYMQILIFVVTFLVMFGLTLFISRSRLG 180
           V+LSQDSK+K+IP L+PG+F FG      V+ISYMQIL+FVVT +VM  LT FISRSRLG
Sbjct: 121 VLLSQDSKDKSIPNLIPGSFSFGPGGAQEVLISYMQILVFVVTLVVMLCLTTFISRSRLG 180

Query: 181 RACRACAEDLKMTNLLGINSNNIIALTFVIGAALAAVAAVLLGMQYGVINPGIGFLAGIK 240
           RACRACAED++M NLLGIN+NNIIALTFVIGAALAAVAAVLL MQYGVINP  GFL G+K
Sbjct: 181 RACRACAEDIRMANLLGINTNNIIALTFVIGAALAAVAAVLLSMQYGVINPNAGFLVGLK 240

Query: 241 AFTAAVLGGIGSIPGAMLGGLLLGVAEAFGADVFGDQYKDVVAFGLLILVLLFRPTGILG 300
           AFTAAVLGGIGSIPGAMLGGL+LGVAEAFGAD+FGDQYKDVVAFGLL+LVLLFRPTG+LG
Sbjct: 241 AFTAAVLGGIGSIPGAMLGGLVLGVAEAFGADIFGDQYKDVVAFGLLVLVLLFRPTGLLG 300

Query: 301 RPEVEKV 307
           RPEVEKV
Sbjct: 301 RPEVEKV 307


Lambda     K      H
   0.328    0.145    0.413 

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: 454
Number of extensions: 7
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: 307
Length of database: 307
Length adjustment: 27
Effective length of query: 280
Effective length of database: 280
Effective search space:    78400
Effective search space used:    78400
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 (21.7 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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