GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocE in Pseudomonas simiae WCS417

Align arginine permease (characterized)
to candidate GFF4342 PS417_22235 aromatic amino acid transporter

Query= CharProtDB::CH_091699
         (590 letters)



>FitnessBrowser__WCS417:GFF4342
          Length = 473

 Score =  246 bits (627), Expect = 2e-69
 Identities = 153/471 (32%), Positives = 241/471 (51%), Gaps = 31/471 (6%)

Query: 81  NAEVKRELKQRHIGMIALGGTIGTGLFIGLSTPLTNAGPVGALISYLFMGSLAYSVTQSL 140
           + E+KR LK RHI +IALGG IGTGLF+G +  L +AGP   ++ Y   G +A+ + + L
Sbjct: 8   SGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGP-SMILGYAICGFIAFMIMRQL 66

Query: 141 GEMATFIPVTSSFTVFSQRFLSPAFGAANGYMYWFSWAITFALELSVVGQVIQFWTYKVP 200
           GEM    PV  SF+ F+ ++     G  +G+  W  + +    EL+ VG+ + +W  ++P
Sbjct: 67  GEMIVEEPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYVHYWWPEIP 126

Query: 201 LAAWISIFWVIITIMNLFPVKYYGEFEFWVASIKVLAIIGFL-IYCFCMVCGAGVTGPVG 259
                + F+V+I ++NL  VK +GE EFW A IKV+AI+G + +  + +V G G      
Sbjct: 127 TWVSAAAFFVLINLINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGTGGPQASV 186

Query: 260 FRYWRNPGAWGPGIISKDKNEGRFLGWVSSLINAAFTFQGTELVGITAGEAANPRKSVPR 319
              W + G +  G+           G V ++    F+F G E++G TA EA  PR  +P+
Sbjct: 187 TNLWEHGGFFPHGV----------GGLVMAMAIIMFSFGGLEMLGFTAAEADKPRTVIPK 236

Query: 320 AIKKVVFRILTFYIGSLLFIGLLVPYND--PKLTQSTSYVSTSPFIIAIENSGTKVLPHI 377
           AI +V++RIL FYIG+L+ +  L P++     L  S    S SPF+      G+    HI
Sbjct: 237 AINQVIYRILIFYIGALVVLLSLTPWDSLLATLNASGDAYSGSPFVQVFSMLGSDTAAHI 296

Query: 378 FNAVILTTIISAANSNIYVGSRILFGLSKNKLAPKFLSRTTKGGVPYIAVFVTAAFGALA 437
            N V+LT  +S  NS  Y  SR+L G+++   APK L++  K GVP  ++  +AA   +A
Sbjct: 297 LNFVVLTAALSVYNSGTYCNSRMLLGMAEQGDAPKALAKIDKRGVPVRSILASAAITLVA 356

Query: 438 YMETSTGGDKVFEWLLNITGVAGFFAWLFISISHIRFMQALKYRGISRDELP-FKAKLMP 496
            +          E L+++        W  IS SH +F Q +   G    ++P FKA   P
Sbjct: 357 VLMNYLIPQHALELLMSLVVATLVINWAMISFSHFKFRQHMNRTG----QVPLFKALWYP 412

Query: 497 GLAYYAATFMTIIIIIQGFTAFAPKFNGVSFAAAYISIFLFLAVWILFQCI 547
              Y    F+  I++I            +      +S+F  + VW++F  +
Sbjct: 413 YGNYVCLAFVVFILVIM-----------LMIPGIQVSVFA-IPVWVMFMAV 451


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: 39
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: 473
Length adjustment: 35
Effective length of query: 555
Effective length of database: 438
Effective search space:   243090
Effective search space used:   243090
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.

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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