GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Pseudomonas fluorescens FW300-N1B4

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Pf1N1B4_1381 High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1)

Query= uniprot:Q1MCU0
         (300 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1381
          Length = 304

 Score =  308 bits (790), Expect = 8e-89
 Identities = 154/301 (51%), Positives = 218/301 (72%), Gaps = 5/301 (1%)

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

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

Query: 124 GPRNKPIPPMVSSVYQF----GNISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQRAT 179
           G R + +P +++  ++     G + ++  +I I+V   V + +  Y++  T LGR  RAT
Sbjct: 124 GARQQGVPTLLTGAWRVEVGTGFVQLTYTKIFILVAAFVGMALLTYVIKYTKLGRMCRAT 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  VL+F+P G+LGRP V K
Sbjct: 244 LGGIGSLPGAMLGGIILGISESLFSGLVNSDYKDVFSFSLLVLVLVFRPQGLLGRPLVSK 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: 380
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 (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