GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Bap2 in Pantoea rwandensis LMG 26275

Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate WP_084937109.1 HA51_RS22655 amino acid permease

Query= TCDB::Q2VQZ4
         (536 letters)



>NCBI__GCF_002095475.1:WP_084937109.1
          Length = 488

 Score =  303 bits (777), Expect = 7e-87
 Identities = 166/480 (34%), Positives = 257/480 (53%), Gaps = 15/480 (3%)

Query: 32  GLKQDLKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIGIMLLCTCLALAE 91
           GL+++LK RH+ MIAIGG+IG GLFV SG  + + GP   L+ Y +IG+M+     +L E
Sbjct: 12  GLRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYALIGLMVYFLMTSLGE 71

Query: 92  MAVLYPVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASITIRFWREDINMA 151
           +A   PV+G+F TY  ++V+  +GFA+GW Y   W   +  +L+A+ + + +W  D    
Sbjct: 72  LAAFMPVSGSFATYGSKYVEEGFGFALGWNYWYNWAVTIAVDLVASQLVMNYWFPDTPGW 131

Query: 152 VWVSVFLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINCGGVGDQGYIGVK 211
           +W ++FL ++  +    V+G+GE E+  S+IK+   V FI++G+++  G +      G  
Sbjct: 132 IWSALFLCLMFLLNYISVKGFGEAEYWFSLIKVVTVVIFIVVGVLMITGIMRGAENAGWH 191

Query: 212 YWR--DPGAFTSFKGFCAVFVVAAFSFGGTEMVGLAAAESANPRKSIPMASKQVFWRIAI 269
            W   D      F     V ++  FSF GTE++G+AA ES +P K+IP A +QVFWRI +
Sbjct: 192 NWTVGDAPFAGGFAAMIGVAMIVGFSFQGTELIGIAAGESQDPAKNIPRAVRQVFWRILL 251

Query: 270 FYILNLFIVGLILPANDPRLMGASGANTKASPFVLAIQDAGIKVLPSIMNAVITVAVLSV 329
           FYI  + I+ LILP  DP+L+     +   SPF L  Q+AG+    ++MNAVI  AVLS 
Sbjct: 252 FYIFAILIISLILPYTDPKLLHNDVTDIAISPFTLVFQNAGLLSAAAVMNAVILTAVLSA 311

Query: 330 ANSCTFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIAFGLLAYIGAAPQGMEIF 389
            NS  + STR +  +A    AP  F  +   G P   +I       L ++ +     E++
Sbjct: 312 GNSGMYASTRMLFNLAREGKAPRIFGKLSKGGVPRNALIATTVVAGLCFLSSKFGNQEVY 371

Query: 390 GWLLALTGLGFLFVWGSICLAHIRMRAGMKAQGINLGLIPYKTPFGVAGSYLGLGLNILA 449
            WLL  +G+     W  I ++H R R G  AQG+NL  +PY++ F   G      L ++ 
Sbjct: 372 LWLLNTSGMTGFIAWLGIAISHYRFRRGYVAQGLNLADLPYRSGFFPLGPIFAFVLCLII 431

Query: 450 LIASFYTALFPAS----GASPTAEAFFSSYLAFFSVTLLYLGYKACTRKRQMYVRPAEMD 505
            +   Y A         G + T       Y+      L++LGYK     R  +V+ +EM+
Sbjct: 432 TLGQNYQAFLQDRIDWYGVAAT-------YIGIPLFLLIWLGYKLVRGSR--WVKYSEME 482


Lambda     K      H
   0.327    0.142    0.442 

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: 643
Number of extensions: 26
Number of successful extensions: 2
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: 536
Length of database: 488
Length adjustment: 35
Effective length of query: 501
Effective length of database: 453
Effective search space:   226953
Effective search space used:   226953
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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