GapMind for catabolism of small carbon sources

 

Alignments for a candidate for permease in Pseudomonas simiae WCS417

Align histidine permease (characterized)
to candidate GFF4632 PS417_23700 aromatic amino acid transporter

Query= reanno::pseudo3_N2E3:AO353_12275
         (468 letters)



>FitnessBrowser__WCS417:GFF4632
          Length = 467

 Score =  381 bits (979), Expect = e-110
 Identities = 193/453 (42%), Positives = 283/453 (62%), Gaps = 13/453 (2%)

Query: 7   GLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRALGEM 66
           GLKRGL  RHI+ +ALG AIGTGLF GSA  ++ AGP+++L Y I G   F++MR LGEM
Sbjct: 10  GLKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAFLIMRQLGEM 69

Query: 67  AVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPEVSRWI 126
            V  PVAGSF  +A  Y G  AGF+ GW Y    V+VGMA++TA G Y+ FW+P++  W+
Sbjct: 70  IVEEPVAGSFSHFAHKYWGGYAGFLAGWNYWVLYVLVGMAELTAVGKYIQFWWPDIPTWV 129

Query: 127 WVLGVVSIVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAPGQVTDI 186
             L     V  +N  NVK FGE EFW +++KV AIV MI+ G  ++  G     G    +
Sbjct: 130 SALVFFVAVNLINTLNVKFFGETEFWFAIIKVVAIVGMIVLGCYLLFSGTG---GPQASV 186

Query: 187 SNLWTQGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAINAVPLRIL 246
           SNLW+ GGF PNG  GL+ S A +MF+FGG+E++G+TA EA +P+ V+P+AIN V  RIL
Sbjct: 187 SNLWSHGGFFPNGGMGLLMSMAFIMFSFGGLELVGITAAEASEPRKVIPKAINQVVYRIL 246

Query: 247 LFYVLTMLVLMSIFPWQQI---------GSQGSPFVQIFDKLGISSAATILNIVVITAAI 297
           +FYV  + VL+S++PW Q+            GSPFVQIF  +G  +AA ILN VV+TAA+
Sbjct: 247 IFYVGALTVLLSLYPWDQLLQTLGASGDAYSGSPFVQIFSLIGNDTAAHILNFVVLTAAL 306

Query: 298 SAINSDIFGAGRMMFGLAQQGHAPKGFAHLSRNGVPWMTVVVMSVALLLGVLLNYLIPEN 357
           S  NS ++   RM+FGLA+QG APK    L++ GVP   + + ++  +L V++NY+ P++
Sbjct: 307 SVYNSGVYCNSRMLFGLAEQGDAPKSLMKLNKQGVPIRALAISALVTMLCVVVNYVAPQS 366

Query: 358 VFLLIASIATFATVWVWLMILFTQVAMRRSMTAEQVAQLKFPVPFWPYAPMAAIAFMLFV 417
              L+ ++   + +  W +I  T +  R++M  EQ     F   ++P++    +AFM+ +
Sbjct: 367 ALELLFALVVASLMINWALISITHIKFRKAM-GEQGVTPSFKTFWFPFSNYLCLAFMVMI 425

Query: 418 FGVLGYFPDTQAALIVGVVWIVLLVLAYLMWVK 450
             V+   P    ++    VW+ ++ +AY + V+
Sbjct: 426 ISVMLAIPGISESVYAMPVWVGIIYVAYRLRVR 458


Lambda     K      H
   0.329    0.142    0.441 

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: 650
Number of extensions: 36
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: 468
Length of database: 467
Length adjustment: 33
Effective length of query: 435
Effective length of database: 434
Effective search space:   188790
Effective search space used:   188790
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 (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