GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livH in Desulfovibrio vulgaris Hildenborough

Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate 208249 DVU2743 high-affinity branched-chain amino acid ABC ransporter, permease protein

Query= TCDB::Q8DQI0
         (292 letters)



>lcl|MicrobesOnline__882:208249 DVU2743 high-affinity branched-chain
           amino acid ABC ransporter, permease protein
          Length = 306

 Score =  243 bits (619), Expect = 5e-69
 Identities = 133/299 (44%), Positives = 191/299 (63%), Gaps = 14/299 (4%)

Query: 1   MNLMLQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYFLIN----- 55
           M   +Q + N L  GS YAL+ALGYT+VYG++ LINFAHGDI+M+GA+I +F+ +     
Sbjct: 1   METFIQNIFNALQWGSFYALIALGYTLVYGVLLLINFAHGDIFMVGAYISFFVASILLGQ 60

Query: 56  -------SFQMNFFVALIVAMLATAILGVVIEFLAYRPLRH--STRIAVLITAIGVSFLL 106
                  S  M   + + + M+ TA +GV +E +AYRPLR   + R+ V+ITA+    +L
Sbjct: 61  IGGFFELSGPMALALTVPLTMVLTAGVGVTLERVAYRPLRRKGAHRLYVVITALMCGIML 120

Query: 107 EYGMVYLVGANTRAFPQAIQTVRYDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGK 166
           E G + L+GA+ +A P+ I  V Y +G +S+TN++LM++  + ++  LLQ IV +T++G 
Sbjct: 121 ENGNLALLGASRKALPEMIDKVVYTIGTVSVTNLKLMVIVTAFLVFALLQFIVTRTRIGM 180

Query: 167 AMRAVSVDSDAAQLMGINVNRTISFTFALGSALAGAAGVLIALYYNSLEPLMGVTPGLKS 226
           AMRAV+ D  A  LMGI ++  I FTF LGS  AG AG+L A+ Y  L+P MG   G K+
Sbjct: 181 AMRAVAWDKFALPLMGIPLDSIIVFTFVLGSGFAGLAGLLFAMSYPILDPYMGAMVGWKA 240

Query: 227 FVAAVLGGIGIIPGAALGGFVIGLLETFATAFGMSDFRDAIVYGILLLILIVRPAGILG 285
           F+AAV+GGIG I GA +GGF++  +E    A   S FRD   + ILL I+  RP G+ G
Sbjct: 241 FIAAVVGGIGDIRGAFIGGFLLAFIEIMVAAVFPSTFRDLFAFSILLFIMWQRPTGLFG 299


Lambda     K      H
   0.330    0.146    0.407 

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: 230
Number of extensions: 11
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: 292
Length of database: 306
Length adjustment: 27
Effective length of query: 265
Effective length of database: 279
Effective search space:    73935
Effective search space used:    73935
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 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