GapMind for catabolism of small carbon sources

 

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

Align Glutamate transporter homolog; Glt(Ph); Sodium-aspartate symporter Glt(Ph); Sodium-dependent aspartate transporter (characterized)
to candidate N515DRAFT_0019 N515DRAFT_0019 Na+/H+-dicarboxylate symporter

Query= SwissProt::O59010
         (425 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0019
          Length = 438

 Score =  203 bits (516), Expect = 1e-56
 Identities = 147/437 (33%), Positives = 227/437 (51%), Gaps = 57/437 (13%)

Query: 12  VLQKILIGLILGAIVGLILGHY---------GYADAVKTYVKPFGDLFVRLLKMLVMPIV 62
           +LQ +LIG++  AI  L +G +          +A AV   + P G +F+RLL  +V+P+V
Sbjct: 11  ILQGLLIGVV-AAIATLAIGQFHPATLKTMQAFATAV---LDPLGQVFLRLLFFVVIPLV 66

Query: 63  FASLVVGAASISPARLGRVGVKIVVYYLLTSA---FAVTLGIIMARLFNPG--------- 110
           FASL  G A +   RLGR+G      + L +A    AV +G++M  L  PG         
Sbjct: 67  FASLASGVAQLG--RLGRLGPLAARTFALFAANMLIAVAIGLLMMNLLQPGHQLEPGSRE 124

Query: 111 -------AGIHLAVGGQQFQPKQAPPLVKILLDIVPTNPFGAL------ANGQVLPTIFF 157
                   G H A+  +Q QP  +  L   +   +P N  GA       A G VLP I F
Sbjct: 125 RLLQEYGGGAHRAMERRQQQPDMS--LATAVDMFMPRNLLGAFVGHDRGALGDVLPLILF 182

Query: 158 AIILGIAITYLMNSENEKVRKSAETLLDAINGLAEAMYKIVNGVMQYAPIGVFALIAYVM 217
           AI++G A T L   +  K++   + L + + G       IV   ++ AP+ V A+I  V+
Sbjct: 183 AILVGAAATLLDEDKRLKLQSGLDLLSELMTG-------IVGFALRLAPVAVPAMIYSVI 235

Query: 218 AEQGVKVVGELAKVTAAVYVGLTLQILLVYFVLLKIYGI-DPISFIKKAKDAMLTAFVTR 276
            + G  V+  L+  TA   + L L +     + L++     P+++ ++ +  ++TAF T 
Sbjct: 236 VKIGTGVLLTLSVFTAGCALALALHLFGSLSLWLRLLARRSPLAYFRQIRPVLITAFSTS 295

Query: 277 SSSGTLPVTMRVAK-EMGISEGIYSFTLPLGATINMDGTALYQGVCTFFIANALGSHLTV 335
           SSS TLP ++ +A+ E+ +      F LPLGAT+NM GTAL++G    F+A A G  LT+
Sbjct: 296 SSSATLPASLALARDELRLRPSTAGFVLPLGATMNMSGTALFEGCVVLFVAQAFGVDLTL 355

Query: 336 GQQLTIVLTAVLASIGTAGVPGAGAIMLAMVLESVGLPLTDPNVAAAYAMILGIDAILDM 395
           GQQ  ++L AVL+++  AG+PG    ++A +L + G+P           ++LG+D ILDM
Sbjct: 356 GQQCVLMLLAVLSAVAVAGIPGGSLPLIAGLLATFGVP------PEGIGLVLGVDRILDM 409

Query: 396 GRTMVNVTGDLTGTAIV 412
            RT VNV  DL    +V
Sbjct: 410 LRTTVNVGSDLVTATVV 426


Lambda     K      H
   0.325    0.141    0.396 

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: 436
Number of extensions: 24
Number of successful extensions: 6
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: 425
Length of database: 438
Length adjustment: 32
Effective length of query: 393
Effective length of database: 406
Effective search space:   159558
Effective search space used:   159558
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: 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