GapMind for catabolism of small carbon sources

 

Aligments for a candidate for araH in Paraburkholderia bryophila 376MFSha3.1

Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate H281DRAFT_02330 H281DRAFT_02330 L-arabinose ABC transporter membrane protein

Query= CharProtDB::CH_014278
         (328 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_02330 H281DRAFT_02330
           L-arabinose ABC transporter membrane protein
          Length = 334

 Score =  317 bits (811), Expect = 3e-91
 Identities = 162/324 (50%), Positives = 230/324 (70%), Gaps = 3/324 (0%)

Query: 5   STSGSGAPKSSFSFGRIWD---QYGMLVVFAVLFIACAIFVPNFATFINMKGLGLAISMS 61
           ST    +   S    R WD   + G+++VF +LF   +  VP+F +  N++GL L++++ 
Sbjct: 9   STPAVASAGLSARAARTWDLINKSGIVMVFIILFAVLSFTVPDFLSSRNIQGLLLSVTLI 68

Query: 62  GMVACGMLFCLASGDFDLSVASVIACAGVTTAVVINLTESLWIGVAAGLLLGVLCGLVNG 121
           G ++  M+F LA G+ DLSVAS++A AGV  + +I +T S+ +GVAAG+L G   GLVNG
Sbjct: 69  GSISVTMMFVLALGEVDLSVASIVAFAGVVASTLITVTHSVLLGVAAGVLAGGAVGLVNG 128

Query: 122 FVIAKLKINALITTLATMQIVRGLAYIISDGKAVGIEDESFFALGYANWFGLPAPIWLTV 181
            ++A+ KIN+LI TLA M++VRGLA+I S G AV I +E FF LG  ++ G+  PIW  +
Sbjct: 129 VLVARYKINSLIVTLAMMEVVRGLAFITSSGDAVMISEERFFDLGGGSFLGISYPIWSNI 188

Query: 182 ACLIIFGLLLNKTTFGRNTLAIGGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILAS 241
              ++FG LL KT FG+N LA+GGN EAA LAG+PV R KI +FVL GLV+  AG++LAS
Sbjct: 189 IGFVVFGFLLKKTVFGKNVLAVGGNSEAALLAGLPVTRIKITVFVLQGLVTGFAGVMLAS 248

Query: 242 RMTSGQPMTSIGYELIVISACVLGGVSLKGGIGKISYVVAGILILGTVENAMNLLNISPF 301
           RM+ G P TS+G EL VISACVLGGVSL GG+  IS V+ G+LI+G+V++AM+L+N+  F
Sbjct: 249 RMSLGDPKTSVGLELGVISACVLGGVSLTGGVATISGVLVGVLIMGSVQDAMSLMNVPTF 308

Query: 302 AQYVVRGLILLAAVIFDRYKQKAK 325
            QY++RG ILL AV+FD++++  +
Sbjct: 309 YQYLIRGGILLLAVLFDQFRRSKR 332


Lambda     K      H
   0.327    0.141    0.414 

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: 389
Number of extensions: 22
Number of successful extensions: 1
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: 328
Length of database: 334
Length adjustment: 28
Effective length of query: 300
Effective length of database: 306
Effective search space:    91800
Effective search space used:    91800
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 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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, 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