GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ansP in Pseudomonas simiae WCS417

Align Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized)
to candidate GFF4342 PS417_22235 aromatic amino acid transporter

Query= TCDB::P40812
         (497 letters)



>FitnessBrowser__WCS417:GFF4342
          Length = 473

 Score =  324 bits (830), Expect = 5e-93
 Identities = 171/467 (36%), Positives = 282/467 (60%), Gaps = 20/467 (4%)

Query: 28  KAMGNRQVQMIAIGGAIGTGLFLGAGARLQMAGPALALVYLICGIFSFFILRALGELVLH 87
           + + NR +Q+IA+GGAIGTGLFLG+   L+ AGP++ L Y ICG  +F I+R LGE+++ 
Sbjct: 13  RGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAFMIMRQLGEMIVE 72

Query: 88  RPSSGSFVSYAREFLGEKAAYVAGWMYFINWAMTGIVDITAVALYMHYWGAFGDVPQWVF 147
            P +GSF  +A ++ G  A +++GW  +I + + G+ ++TAV  Y+HYW  + ++P WV 
Sbjct: 73  EPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYVHYW--WPEIPTWVS 130

Query: 148 ALGALTIVGTMNMIGVKWFAEMEFWFALIKVLAIVIFLVVGTIFL--GTGQPLEGNATGF 205
           A     ++  +N+  VK F E EFWFA+IKV+AIV  + +G+  L  GTG P + + T  
Sbjct: 131 AAAFFVLINLINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLVSGTGGP-QASVTN- 188

Query: 206 HLITDNGGFFPHGLLPALVLIQGVVFAFASIELVGTAAGECKDPQKMVPKAINSVIWRIG 265
             + ++GGFFPHG+   ++ +  ++F+F  +E++G  A E   P+ ++PKAIN VI+RI 
Sbjct: 189 --LWEHGGFFPHGVGGLVMAMAIIMFSFGGLEMLGFTAAEADKPRTVIPKAINQVIYRIL 246

Query: 266 LFYVGSVVLLVLLLPWNAYQA---------GQSPFVTFFSKLGVPYIGSIMNIVVLTAAL 316
           +FY+G++V+L+ L PW++  A           SPFV  FS LG      I+N VVLTAAL
Sbjct: 247 IFYIGALVVLLSLTPWDSLLATLNASGDAYSGSPFVQVFSMLGSDTAAHILNFVVLTAAL 306

Query: 317 SSLNSGLYCTGRILRSMSMGGSAPKFMAKMSRQHVPYAGILATLVVYVVGVFLNYLVPSR 376
           S  NSG YC  R+L  M+  G APK +AK+ ++ VP   ILA+  + +V V +NYL+P  
Sbjct: 307 SVYNSGTYCNSRMLLGMAEQGDAPKALAKIDKRGVPVRSILASAAITLVAVLMNYLIPQH 366

Query: 377 VFEIVLNFASLGIIASWAFIMVCQMRLRQAIKEGKAADVSFKLPGAPFTSWLTLLFLLSV 436
             E++++     ++ +WA I     + RQ +       + FK    P+ +++ L F++ +
Sbjct: 367 ALELLMSLVVATLVINWAMISFSHFKFRQHMNRTGQVPL-FKALWYPYGNYVCLAFVVFI 425

Query: 437 LVLMAFDYPNGTYTIASLPLIAILLVAGWFGVRRRVAEIHRTAPVTA 483
           LV+M    P    ++ ++P + ++ +A  +G++ + +     AP  +
Sbjct: 426 LVIMLM-IPGIQVSVFAIP-VWVMFMAVCYGIKNKRSAQQALAPAAS 470


Lambda     K      H
   0.328    0.140    0.434 

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: 623
Number of extensions: 31
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: 497
Length of database: 473
Length adjustment: 34
Effective length of query: 463
Effective length of database: 439
Effective search space:   203257
Effective search space used:   203257
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