GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livH in Klebsiella michiganensis M5al

Align ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate BWI76_RS05990 BWI76_RS05990 branched-chain amino acid ABC transporter permease

Query= TCDB::Q8DQI0
         (292 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS05990 BWI76_RS05990 branched-chain
           amino acid ABC transporter permease
          Length = 299

 Score =  251 bits (640), Expect = 2e-71
 Identities = 131/293 (44%), Positives = 197/293 (67%), Gaps = 5/293 (1%)

Query: 3   LMLQQLVNGLILGSVYALLALGYTMVYGIIKLINFAHGDIYMMGAFIGYFLINSFQMNFF 62
           + LQQ+VNG+ LG +YAL+A+GYTMVYG+++LINFAH D+ M+GAF   FL +S  + F 
Sbjct: 5   IFLQQVVNGMSLGGMYALIAIGYTMVYGVLRLINFAHADVMMVGAFTTLFLFSSIGLPFG 64

Query: 63  VALIVAMLATAILGVVIEFLAYRPLRHSTRIAVLITAIGVSFLLEYGMVYLVGANTRAF- 121
           VA+ + +    + G++I+ +AYRPLR +++I++LITAIGVSF LE     L G ++R F 
Sbjct: 65  VAVFLTLALCGLFGMLIDRVAYRPLRQASKISMLITAIGVSFFLENLFNVLFGGSSRFFS 124

Query: 122 -PQAIQTVRYDLGPISLTNVQLMILGISLILMILLQVIVQKTKMGKAMRAVSVDSDAAQL 180
            P      R   G + +TNV  ++  I+++L++ +  ++ +T+ G A+RAV+ D +  +L
Sbjct: 125 APDFFNNTR-AFGDVIITNVAWIVPLITVLLLLAILWLLYRTRYGMAIRAVAFDVNTVRL 183

Query: 181 MGINVNRTISFTFALGSALAGAAGVLIALYYNSLEPLMGVTPGLKSFVAAVLGGIGIIPG 240
           MGI+ NR IS  FALGS+LA   GV  ++ Y +++PLMGV  GLK+F AAVLGGIG + G
Sbjct: 184 MGIDANRIISLVFALGSSLAALGGVFYSISYPTIDPLMGVLIGLKAFAAAVLGGIGSVTG 243

Query: 241 AALGGFVIGLLETFATAF--GMSDFRDAIVYGILLLILIVRPAGILGKNVKEK 291
           A LGGF++G  E  A A    +  ++DA  +  L+L+L+ RP GI+G    E+
Sbjct: 244 AVLGGFILGFTEVVAVALFPELGGYKDAFAFMFLILVLLFRPVGIMGDERLER 296


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: 246
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: 299
Length adjustment: 26
Effective length of query: 266
Effective length of database: 273
Effective search space:    72618
Effective search space used:    72618
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, 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