GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rocE in Klebsiella michiganensis M5al

Align Amino-acid permease RocE (characterized)
to candidate BWI76_RS04870 BWI76_RS04870 aromatic amino acid transporter AroP

Query= SwissProt::P39137
         (467 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS04870 BWI76_RS04870 aromatic amino
           acid transporter AroP
          Length = 455

 Score =  305 bits (781), Expect = 2e-87
 Identities = 156/434 (35%), Positives = 255/434 (58%), Gaps = 7/434 (1%)

Query: 5   QDNGNQLQRTMKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGGFIMFLTM 64
           Q +G++L+R +K+RH+ +I+LGG IGTG FLG+   I  AGP G +L Y + GFI FL M
Sbjct: 4   QQHGDRLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQNAGP-GIILGYAIAGFIAFLIM 62

Query: 65  LCLGELAVAFPVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLMQRWFP 124
             LGE+ V  PV+GSF  +A K+     GFA GW YW+ + +    E  + G+ +Q W+P
Sbjct: 63  RQLGEMVVEEPVAGSFSHFAYKYWGGFAGFASGWNYWVLYVLVAMAELTAVGKYVQFWWP 122

Query: 125 HIDVWIWCLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILGGAAMFGLIDLKG 184
            I  W+   +F   +  +N    K F E EFWF+ IK++ ++  I+ GG  +F      G
Sbjct: 123 EIPTWVSAAIFFIAINAINLTNVKVFGEMEFWFAIIKVVAVVAMILFGGWLLFSG---NG 179

Query: 185 GEQAPFLTHFYEDGLFPNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKTIPRSIKQ 244
           G QA     + + G  P+G   +++ M  + F+F G EL+G+ A E+++PE++IP++  Q
Sbjct: 180 GPQATVRNLWEQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQ 239

Query: 245 TVWRTLVFFVLSIIVIAGMIPWKQAGVVESPFVAVFEQIGIPYAADIMNFVILIALLSVA 304
            ++R L+F+V S+ V+  ++PW +     SPFV +F ++G  + A+ +N V+L A LSV 
Sbjct: 240 VIYRILIFYVGSLAVLLSLLPWSRVTADTSPFVLIFHELGDTFVANALNIVVLTAALSVY 299

Query: 305 NSGLYASTRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLLTKFAQAETVYM 364
           NS +Y ++R+L+ +A +G A KAL   ++RGVP+ +++V+  V  L +L  +   E+ + 
Sbjct: 300 NSCVYCNSRMLFGLAQQGNAPKALMSVDKRGVPVNTILVSALVTALCVLINYFAPESAFG 359

Query: 365 VLLSLAGMSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVLPLIGLTLNTVVL 424
           +L++L   +  + W  ISL+ I FRR   ++G      +F   LYP+   I L     VL
Sbjct: 360 LLMALVVSALVINWAMISLAHIKFRRAKQQQG---VVTRFPALLYPLSNWICLLFMAGVL 416

Query: 425 ISLAFDPEQRIALY 438
           + +   P   I++Y
Sbjct: 417 VIMLMTPGMAISVY 430


Lambda     K      H
   0.329    0.142    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: 533
Number of extensions: 25
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: 467
Length of database: 455
Length adjustment: 33
Effective length of query: 434
Effective length of database: 422
Effective search space:   183148
Effective search space used:   183148
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 (21.8 bits)
S2: 51 (24.3 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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