GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Bap2 in Pseudomonas simiae WCS417

Align Leu/Val/Ile amino-acid permease; Branched-chain amino-acid permease 2 (characterized)
to candidate GFF4632 PS417_23700 aromatic amino acid transporter

Query= SwissProt::P38084
         (609 letters)



>FitnessBrowser__WCS417:GFF4632
          Length = 467

 Score =  216 bits (551), Expect = 1e-60
 Identities = 133/402 (33%), Positives = 219/402 (54%), Gaps = 16/402 (3%)

Query: 91  LKKSMKSRHVVMMSLGTGIGTGLLVANAKGLHYGGPAALIIGYILVSFVTYFMIQAAGEM 150
           LK+ +K+RH+ +++LG  IGTGL + +A  L   GP+ +I+GY +  F+ + +++  GEM
Sbjct: 11  LKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPS-MILGYAIAGFIAFLIMRQLGEM 69

Query: 151 AVTYPTLPANFNAYSSIFISKSFGFATVWLYCFQWLTVLPLELITASMTIQFWNDKINPD 210
            V  P +  +F+ ++  +     GF   W Y   ++ V   EL      IQFW   I   
Sbjct: 70  IVEEP-VAGSFSHFAHKYWGGYAGFLAGWNYWVLYVLVGMAELTAVGKYIQFWWPDIPTW 128

Query: 211 IYILIFYVFLVFIHFFGVKAYGETEFIFNCCKILMIAGFIILSIVINCGGAGNDGYIGAT 270
           +  L+F+V +  I+   VK +GETEF F   K++ I G I+L   +   G G      + 
Sbjct: 129 VSALVFFVAVNLINTLNVKFFGETEFWFAIIKVVAIVGMIVLGCYLLFSGTGGPQASVSN 188

Query: 271 YWHNPGAFAGDTSIGRFKNVCYILVTAYFSFGGMELFALSVQEQSNPRKSTPVAAKRSIY 330
            W + G F  +  +G   ++ +I+    FSFGG+EL  ++  E S PRK  P A  + +Y
Sbjct: 189 LWSH-GGFFPNGGMGLLMSMAFIM----FSFGGLELVGITAAEASEPRKVIPKAINQVVY 243

Query: 331 RIVVIYLLTMILIGFNVPYNDD-QLMGAGGSATHASPYVLAASIHGVKIVPHIINAVILI 389
           RI++ Y+  + ++    P++   Q +GA G A   SP+V   S+ G     HI+N V+L 
Sbjct: 244 RILIFYVGALTVLLSLYPWDQLLQTLGASGDAYSGSPFVQIFSLIGNDTAAHILNFVVLT 303

Query: 390 SVVSVANSSLYAGPRLICSLAQQGYAPKFLDYVDREGRPLRAL----IVCCVFGVIAFVA 445
           + +SV NS +Y   R++  LA+QG APK L  ++++G P+RAL    +V  +  V+ +VA
Sbjct: 304 AALSVYNSGVYCNSRMLFGLAEQGDAPKSLMKLNKQGVPIRALAISALVTMLCVVVNYVA 363

Query: 446 ASSKEEIVFTWLAAIAGLSELFTWTSIMLSHLRFRQAMKVQG 487
             S  E++F  + A    S +  W  I ++H++FR+AM  QG
Sbjct: 364 PQSALELLFALVVA----SLMINWALISITHIKFRKAMGEQG 401


Lambda     K      H
   0.325    0.139    0.423 

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: 747
Number of extensions: 35
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 609
Length of database: 467
Length adjustment: 35
Effective length of query: 574
Effective length of database: 432
Effective search space:   247968
Effective search space used:   247968
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