GapMind for catabolism of small carbon sources

 

Aligments for a candidate for braD in Pseudomonas fluorescens FW300-N2E2

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Pf6N2E2_3579 High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1)

Query= uniprot:Q1MCU0
         (300 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3579 High-affinity
           branched-chain amino acid transport system permease
           protein LivH (TC 3.A.1.4.1)
          Length = 304

 Score =  305 bits (781), Expect = 8e-88
 Identities = 152/301 (50%), Positives = 214/301 (71%), Gaps = 5/301 (1%)

Query: 4   FVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSIFAG 63
           F+QQL+NGLTLGS+YGL+AIGYTMVYGIIGMINFAHG+++M+  + A I  L L + F  
Sbjct: 5   FLQQLINGLTLGSVYGLIAIGYTMVYGIIGMINFAHGEVYMISAYLAAIS-LALLAYFGI 63

Query: 64  LPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQVTQ 123
               +++L  LV  +++T ++ W IERVAY+PLR S RLAPLI+AIG+S+ L N+ Q++Q
Sbjct: 64  ESFPLMILGTLVFTVVVTGVYGWVIERVAYKPLRNSTRLAPLISAIGISLILQNYAQISQ 123

Query: 124 GPRNKPIPPMVSSVYQF----GNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRAT 179
           G R + +P ++    +     G + ++  +I I++     + +  YI+  T LGR  RAT
Sbjct: 124 GARQQGVPTLLEGAMRLDIGSGFVQLTYTKIFILIAAFAGMAVLTYIIKYTKLGRMCRAT 183

Query: 180 EQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFTAAV 239
           +QDRKMA++LG+N D+ IS  F++GAA+AA+AG +  M YG   F  GF  G+KAFTAAV
Sbjct: 184 QQDRKMASILGINTDRVISYVFIIGAAMAALAGVLITMNYGTFDFYAGFIIGIKAFTAAV 243

Query: 240 LGGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILGRPEVEK 299
           LGGIGSLPGA+ GG+++G+ ESL+S      YKDV +F++L  +LIF+P G+LGRP V K
Sbjct: 244 LGGIGSLPGAMLGGIILGISESLFSGLINSDYKDVFSFSLLVLILIFRPQGLLGRPLVAK 303

Query: 300 V 300
           V
Sbjct: 304 V 304


Lambda     K      H
   0.329    0.143    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: 381
Number of extensions: 16
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: 300
Length of database: 304
Length adjustment: 27
Effective length of query: 273
Effective length of database: 277
Effective search space:    75621
Effective search space used:    75621
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