GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livH in Desulfovibrio vulgaris Miyazaki F

Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate 8500415 DvMF_1165 inner-membrane translocator (RefSeq)

Query= TCDB::Q8DQI0
         (292 letters)



>FitnessBrowser__Miya:8500415
          Length = 306

 Score =  244 bits (623), Expect = 2e-69
 Identities = 136/299 (45%), Positives = 191/299 (63%), Gaps = 14/299 (4%)

Query: 1   MNLMLQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYF-------- 52
           M + +Q L N L  GS YAL+ALGYT+VYG++ LINFAHGDI+M+GA+I +F        
Sbjct: 1   MEIFIQNLFNALQWGSFYALIALGYTLVYGVLLLINFAHGDIFMVGAYIAFFVSSLLLGD 60

Query: 53  LINSFQMNFFVALIVA----MLATAILGVVIEFLAYRPLRH--STRIAVLITAIGVSFLL 106
           L+  F +  + AL +     ML TA +GV +E +AYRPLR   + R+ V+ITA+    +L
Sbjct: 61  LLGVFNLPGWAALALTVPLTMLLTAGVGVTLERIAYRPLRRKGAHRLYVVITALMCGLIL 120

Query: 107 EYGMVYLVGANTRAFPQAIQTVRYDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGK 166
           E G + L+GA+ R  P  +  V Y  G +S+TN+++ ++  + ++  LLQ IV +T++G 
Sbjct: 121 ENGNLALLGASRRKLPDMVDKVVYTFGSVSVTNLKVWVIITAFLVFFLLQFIVTRTRIGM 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    AF  S FRD   + ILL+IL  RP G+ G
Sbjct: 241 FIAAVVGGIGDIRGAFIGGFLLAFIEIMVAAFLPSTFRDLFAFTILLMILWQRPTGLFG 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: 241
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: 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:

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