GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysP in Pseudomonas fluorescens GW456-L13

Align Probable lysine/arginine permease CAN2; Basic amino acids permease CAN2 (characterized)
to candidate PfGW456L13_4400 Aromatic amino acid transport protein AroP

Query= SwissProt::Q59WU0
         (568 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4400
          Length = 473

 Score =  234 bits (598), Expect = 4e-66
 Identities = 147/465 (31%), Positives = 236/465 (50%), Gaps = 32/465 (6%)

Query: 56  EVKRDLKARHVSMIAIGGTIGTGLFISTGSLLHTTGPVMSLISFLFVTTLAYSVTQSLGE 115
           E+KR LK RH+ +IA+GG IGTGLF+ +  +L + GP M ++ +     +A+ + + LGE
Sbjct: 10  ELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSM-ILGYAICGFIAFMIMRQLGE 68

Query: 116 MTTYIPVSGSFAQFITRWVSKSCGAANGWLYWFSWAITFALELSVVGQVIQYWTDAVPLA 175
           M    PV+GSF+ F  ++     G  +GW  W  + +    EL+ VG+ I YW   +P  
Sbjct: 69  MIVEDPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHYWAPDIPTW 128

Query: 176 GWISIFFVLLTTFNLFPVKYYGEVEFWIASTKVIAIVGWL-IYAFCMVCGAGKTGPVGFR 234
              + FFVL+   NL  VK +GE EFW A  KV+AIVG + + ++ +V G G        
Sbjct: 129 ASAAAFFVLINAINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGNGGPQAAVSN 188

Query: 235 YWRNGYAWGDGMIVSNNGKYAISFINGLINAVFTFQGTELVAVTAGEAS--PRAIRSAIK 292
            W +G  + +G+        A++FI      +F+F G E++  TA EA      I  AI 
Sbjct: 189 LWSHGGFFPNGV---TGLVMAMAFI------MFSFGGLEMLGFTAAEADKPKTVIPKAIN 239

Query: 293 KVMFRILVFYVLCMLFIGLLVPYND--PKLTQDGGFTRNSPFLIAMENSGTKVLPHIFNA 350
           +V++RIL+FY+  ++ +  L P++     L   G     SPF+      G+    HI N 
Sbjct: 240 QVIYRILIFYIGALVILLSLTPWDSLLTTLNASGDSYSGSPFVQVFSMLGSNTAAHILNF 299

Query: 351 VIVTTIISAGNSNVYSGSRILYGLAQAGVAPKFFLKTNKGGVPYFAVLFTAAFGALGYLA 410
           V++T  +S  NS  Y  SR+L G+A+ G APK   K +K GVP  ++L +AA   +  L 
Sbjct: 300 VVLTAALSVYNSGTYCNSRMLLGMAEQGDAPKALAKIDKRGVPVRSILASAAVTLIAVLL 359

Query: 411 CSEDGNKAFTWLLNIIATAGLIAWGFISVSHVRFMNVLRKRGLSRDILPYKAFFMPYSAY 470
                + A   L++++    +I W  IS SH +F   + K   ++    +KA + PY  Y
Sbjct: 360 NYLIPHSALELLMSLVVATLVINWAMISYSHFKFRQHMNK---TKQTPLFKALWYPYGNY 416

Query: 471 ----YAIIIIFIVVLIQGFTVFWDFNASDFFTAYISVILFVVLWI 511
               + + I+ +++LI G             + Y   +  V +W+
Sbjct: 417 ICLAFVLFILGVMLLIPGIQT----------SVYAIPVWLVFMWV 451


Lambda     K      H
   0.326    0.141    0.448 

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: 742
Number of extensions: 41
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: 568
Length of database: 473
Length adjustment: 35
Effective length of query: 533
Effective length of database: 438
Effective search space:   233454
Effective search space used:   233454
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 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