GapMind for catabolism of small carbon sources

 

Alignments for a candidate for CAT in Dyella japonica UNC79MFTsu3.2

Align Plastidic cationic amino acid transporter, CAT, of 582 aas and 14 TMSs (characterized)
to candidate N515DRAFT_2924 N515DRAFT_2924 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)

Query= TCDB::ALD51314.1
         (582 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2924
          Length = 492

 Score =  232 bits (592), Expect = 2e-65
 Identities = 148/480 (30%), Positives = 248/480 (51%), Gaps = 36/480 (7%)

Query: 44  ARSGGDMKRSLRWYDLVGFGVGGMVGAGVFVTSGRASSHCAGPAVVLSYAIAGFCALLSA 103
           A     +KR+L    LV  G+G ++GAG+FV +G+A++  AGPA+VLS+  AG    L+A
Sbjct: 23  AHGEATLKRALTARHLVLLGIGAIIGAGIFVITGQAAAEHAGPAIVLSFVFAGIACALAA 82

Query: 104 FCYTEFAVDMPVAGGAFSYIRITFGEFLAFLTGANLIIDYVLSNAAVARSFTGYLCTALG 163
            CY EFA  +PV+G A+SY   T GE++A+  G +L+++Y+ + A VA  ++GY    L 
Sbjct: 83  LCYAEFAAMLPVSGSAYSYSYATLGEYVAWFVGWSLVLEYLFTVATVAAGWSGYFNKLLA 142

Query: 164 IES-------KLRITVNGLP----DGFNE-----IDVVAVLVVLALTVIICYSTRESSVL 207
           + S        L  T+   P    DG  +     I++ AV ++ A+T +      +S+ +
Sbjct: 143 LISGWIGHDVSLPQTLAAAPFTVVDGHIQATGMFINLPAVAIIAAITGLCYVGITQSAFV 202

Query: 208 NMVLTVLHIVFIVFVIVIGFTRGDTKNFTKAGDSNHASGFFPFGASGVFNGAAMVYLSYI 267
           N ++  + +  I+  I       +  N+     ++   G   +G +GV   AA+V+ SYI
Sbjct: 203 NSIIVAIKVTVILLFIAFATKYINPDNWHPFIPASE--GASKYGWAGVGRAAAIVFFSYI 260

Query: 268 GYDAVSTMAEEVKNPVKDIPVGVSGSVILVTVLYCLMAASMSMLLPYDMIDPDAPFSGAF 327
           G+DAVST A E KNP +D+P+G+ GS+IL T+LY ++A  ++ +  + ++    P S A 
Sbjct: 261 GFDAVSTAAGEAKNPQRDMPIGIIGSLILCTILYIIVAGILTGIADFRLLGTPEPVSTAL 320

Query: 328 MGSDGWRWVSNVIGVGAGFGILTSLLVAMLGQARYMCVIGRSSVVPAWFAKVHPKTSTPV 387
                  W+  ++ +GA  G+ + +LV ++GQ R    + R  ++PA F ++H K  TP 
Sbjct: 321 DNYPSLHWLQIIVVIGAVTGLSSVMLVMLMGQPRIFYSMARDGLIPAVFGRIHQKFRTPH 380

Query: 388 NASAFLGICTAAIALFTDLQILLNLVSIGTLFVFYMVANAVIYKRYV------SVGVTNP 441
             +  +G+  AA+    ++ +L  +V++GTL  F  V   V+  RY       +  V  P
Sbjct: 381 VGTVVVGVLAAALGGLFNIGVLGEMVAMGTLLAFATVCIGVLVLRYTRPELPRAFRVPVP 440

Query: 442 WPT--LSYLFCFSLTSILFTLLWQFAPPGKPKAFMLGACTAIAIGVLQLFHYMVPQARKP 499
           W    L  L C +L    F   W++          + A  AI   +  L+ Y   + RKP
Sbjct: 441 WIVCPLGALACMALFLQSFLEHWRW----------MLAWIAIGQAIYFLYGYSHSKLRKP 490


Lambda     K      H
   0.326    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: 708
Number of extensions: 36
Number of successful extensions: 2
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: 582
Length of database: 492
Length adjustment: 35
Effective length of query: 547
Effective length of database: 457
Effective search space:   249979
Effective search space used:   249979
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