GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livH in Pseudomonas fluorescens GW456-L13

Align branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized)
to candidate PfGW456L13_123 High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1)

Query= ecocyc::LIVH-MONOMER
         (308 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_123
          Length = 304

 Score =  338 bits (866), Expect = 1e-97
 Identities = 170/301 (56%), Positives = 225/301 (74%), Gaps = 1/301 (0%)

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

Query: 68  TGWLLVAAGFVGAIVIASAYGWSIERVAYRPVRNSKRLIALISAIGMSIFLQNYVSLTEG 127
           +  LL+    +  IV+ + YGW IERVAY+P+RNS RL  LISAIG+S+ LQNY  +++G
Sbjct: 65  SFPLLMLGTLIFTIVVTAVYGWVIERVAYKPLRNSTRLAPLISAIGISLILQNYAQISQG 124

Query: 128 SRDVALPSLFNGQWVVGHSENFSASITTMQAVIWIVTFLAMLALTIFIRYSRMGRACRAC 187
           ++   +P+L +G W V     F   +T  +  I +  F+ M  LT  I+Y+++GR CRA 
Sbjct: 125 AKQQGVPTLLSGAWRVDIGTGF-VQLTYTKVFILVAAFVGMGLLTYVIKYTKLGRMCRAT 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+LVL+  P G+LGRP V K
Sbjct: 244 LGGIGSLPGAMLGGIILGISESLFSGLVNSDYKDVFSFSLLVLVLVFRPQGLLGRPLVSK 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: 341
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: 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 (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