GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocE in Pseudomonas fluorescens FW300-N2E3

Align arginine permease (characterized)
to candidate AO353_05965 AO353_05965 aromatic amino acid transporter

Query= CharProtDB::CH_091699
         (590 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_05965
          Length = 466

 Score =  260 bits (665), Expect = 8e-74
 Identities = 155/438 (35%), Positives = 235/438 (53%), Gaps = 17/438 (3%)

Query: 78  EVQNAEVKRELKQRHIGMIALGGTIGTGLFIGLSTPLTNAGPVGALISYLFMGSLAYSVT 137
           ++Q   +KR LK RHI +IALGG IGTGLF+G +  L +AGP   ++ Y   G +A+ + 
Sbjct: 5   QLQQGVLKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGP-SMILGYAIAGFIAFLIM 63

Query: 138 QSLGEMATFIPVTSSFTVFSQRFLSPAFGAANGYMYWFSWAITFALELSVVGQVIQFWTY 197
           + LGEM    PV  SF+ F+  +     G  +G+ YW  + +    EL+ VG+ +QFW  
Sbjct: 64  RQLGEMIVEEPVAGSFSHFAHNYWGSFAGFLSGWNYWVLYVLVGMAELTAVGKYVQFWWP 123

Query: 198 KVPLAAWISIFWVIITIMNLFPVKYYGEFEFWVASIKVLAIIGFL-IYCFCMVCGAGVTG 256
           +VP     ++F+V++ ++N   VK +GE EFW A IKV+AIIG + + C+ +V G G   
Sbjct: 124 EVPTWVSAAVFFVLVNLINTMNVKVFGEMEFWFAIIKVVAIIGMIALGCYMLVSGTGGPQ 183

Query: 257 PVGFRYWRNPGAWGPGIISKDKNEGRFLGWVSSLINAAFTFQGTELVGITAGEAANPRKS 316
                 W + G +  G            G + ++    F+F G ELVGITA EA+ PRK 
Sbjct: 184 ASVSNLWSHGGFFPNGT----------NGLLMAMAFIMFSFGGLELVGITAAEASEPRKV 233

Query: 317 VPRAIKKVVFRILTFYIGSLLFIGLLVPYND--PKLTQSTSYVSTSPFIIAIENSGTKVL 374
           +P+AI +VV+R+L FY+G+L  +  L P++     L  S    S SPF+      G+   
Sbjct: 234 IPKAINQVVYRVLIFYVGALTVLLSLYPWDQLLQTLGASGDAYSGSPFVQIFALIGSNTA 293

Query: 375 PHIFNAVILTTIISAANSNIYVGSRILFGLSKNKLAPKFLSRTTKGGVPYIAVFVTAAFG 434
             I N V+LT  +S  NS +Y  SR+L+GL++   APK L +  K GVP  A+ ++A   
Sbjct: 294 AQILNFVVLTAALSVYNSGVYCNSRMLYGLAEQGDAPKSLMKLNKQGVPLRALGISALIT 353

Query: 435 ALAYMETSTGGDKVFEWLLNITGVAGFFAWLFISISHIRFMQALKYRGISRDELPFKAKL 494
            L  +      ++  E L  +   +    W  IS++H++F +A+  RGI      FKA  
Sbjct: 354 MLCVVVNYVAPNEALELLFALVVASLMINWAMISLTHLKFRKAMGQRGIVPG---FKAFW 410

Query: 495 MPGLAYYAATFMTIIIII 512
            P   Y    FM +II +
Sbjct: 411 SPYTNYLCLAFMAMIIYV 428


Lambda     K      H
   0.325    0.140    0.438 

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: 702
Number of extensions: 43
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: 590
Length of database: 466
Length adjustment: 35
Effective length of query: 555
Effective length of database: 431
Effective search space:   239205
Effective search space used:   239205
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.6 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