GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1694 in Cupriavidus basilensis 4G11

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate RR42_RS14415 RR42_RS14415 leucine/isoleucine/valine transporter permease subunit

Query= uniprot:A0A165KER0
         (358 letters)



>FitnessBrowser__Cup4G11:RR42_RS14415
          Length = 424

 Score =  265 bits (676), Expect = 2e-75
 Identities = 163/364 (44%), Positives = 217/364 (59%), Gaps = 49/364 (13%)

Query: 5   KTNWIIGAVALLVLPLILQSFGNAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFY 64
           K  W++ AV L V P          V +A LAL+YV+L LGLNIVVGYAGLLDLGYV FY
Sbjct: 98  KVIWLLLAVGL-VFPFFSS---RGAVDVATLALIYVILGLGLNIVVGYAGLLDLGYVGFY 153

Query: 65  AVGAYLFALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLR 124
           AVG Y +AL+           F   F        W  +P+AA ++A FG +LG P L+LR
Sbjct: 154 AVGGYTYALLNQ--------YFGLTF--------WECLPIAAGMSALFGFVLGFPVLRLR 197

Query: 125 GDYLAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRL-------- 176
           GDYLAIVTLGFGEIIR+ LNNL    +LT GP G+  I    VFG+++ +          
Sbjct: 198 GDYLAIVTLGFGEIIRLLLNNL---TSLTGGPDGVSGIPKPTVFGIEMARSASVEGVKTF 254

Query: 177 -EVFGFDINS---VTLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGIN 232
            E+ G+D +    V   Y L L+LV  ++ +  RL    +GRAW A+REDEIA +++G+N
Sbjct: 255 HELLGWDYSGEHMVIFLYLLALLLVGFTLFVTSRLIRMPMGRAWEALREDEIACRSLGLN 314

Query: 233 TRNMKLLAFGMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVIL 292
              +KL AF +GA+F G+ GA F A QG V+PESF+ +ES +I+A+VVLGG+G   GVIL
Sbjct: 315 PTRIKLSAFTLGAAFAGLGGAFFAARQGLVNPESFTFIESALILAVVVLGGMGSQLGVIL 374

Query: 293 GAVLLSALPEVLRYVAGPLQAMTDGRLDSAILRQLLIALAMIIIMLLRPRGLWPSPEHGK 352
            A+LL+ALPE+ R                A  R L+  L M+++M+ RP+GL P+     
Sbjct: 375 AAILLTALPEMAR--------------GFAEYRMLIFGLVMVLMMMWRPQGLLPASRPHV 420

Query: 353 SLTQ 356
            L Q
Sbjct: 421 ELPQ 424


Lambda     K      H
   0.328    0.144    0.430 

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: 411
Number of extensions: 19
Number of successful extensions: 4
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: 358
Length of database: 424
Length adjustment: 30
Effective length of query: 328
Effective length of database: 394
Effective search space:   129232
Effective search space used:   129232
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: 50 (23.9 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 (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