GapMind for catabolism of small carbon sources

 

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

Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate Pf6N2E2_3579 High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1)

Query= ecocyc::LIVH-MONOMER
         (308 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 =  334 bits (857), Expect = 1e-96
 Identities = 168/301 (55%), Positives = 221/301 (73%), Gaps = 1/301 (0%)

Query: 8   FLQQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMGID 67
           FLQQ+ NG+TLGS Y LIAIGYTMVYGIIGMINFAHGEVYMI +Y++ + +A L   GI+
Sbjct: 5   FLQQLINGLTLGSVYGLIAIGYTMVYGIIGMINFAHGEVYMISAYLAAISLALLAYFGIE 64

Query: 68  TGWLLVAAGFVGAIVIASAYGWSIERVAYRPVRNSKRLIALISAIGMSIFLQNYVSLTEG 127
           +  L++    V  +V+   YGW IERVAY+P+RNS RL  LISAIG+S+ LQNY  +++G
Sbjct: 65  SFPLMILGTLVFTVVVTGVYGWVIERVAYKPLRNSTRLAPLISAIGISLILQNYAQISQG 124

Query: 128 SRDVALPSLFNGQWVVGHSENFSASITTMQAVIWIVTFLAMLALTIFIRYSRMGRACRAC 187
           +R   +P+L  G   +     F   +T  +  I I  F  M  LT  I+Y+++GR CRA 
Sbjct: 125 ARQQGVPTLLEGAMRLDIGSGF-VQLTYTKIFILIAAFAGMAVLTYIIKYTKLGRMCRAT 183

Query: 188 AEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAGMKAFTAAV 247
            +D KMAS+LGINTDRVI+  F+IGAAMAA+AGVL+   YG  + Y GF+ G+KAFTAAV
Sbjct: 184 QQDRKMASILGINTDRVISYVFIIGAAMAALAGVLITMNYGTFDFYAGFIIGIKAFTAAV 243

Query: 248 LGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVMPTGILGRPEVEK 307
           LGGIGS+PGAM+GG+ILGI+E+L S  ++++YKDV SF+LL+L+L+  P G+LGRP V K
Sbjct: 244 LGGIGSLPGAMLGGIILGISESLFSGLINSDYKDVFSFSLLVLILIFRPQGLLGRPLVAK 303

Query: 308 V 308
           V
Sbjct: 304 V 304


Lambda     K      H
   0.328    0.141    0.410 

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: 334
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: 308
Length of database: 304
Length adjustment: 27
Effective length of query: 281
Effective length of database: 277
Effective search space:    77837
Effective search space used:    77837
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, the preprint 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