GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltP in Sphingomonas koreensis DSMZ 15582

Align proton/sodium-glutamate symport protein GltT (characterized)
to candidate Ga0059261_0201 Ga0059261_0201 Na+/H+-dicarboxylate symporters

Query= CharProtDB::CH_088342
         (421 letters)



>FitnessBrowser__Korea:Ga0059261_0201
          Length = 455

 Score =  312 bits (799), Expect = 2e-89
 Identities = 170/411 (41%), Positives = 253/411 (61%), Gaps = 23/411 (5%)

Query: 10  IFIGLILGIIVG-AIFYGNPK---------------VAAYLQPIGDIFLRLIKMIVIPIV 53
           I I L+ G IVG  + YG                  VA Y   +  IFLRLIKMI+ P+V
Sbjct: 9   ILIALVAGAIVGLGLHYGIHNSFGADSAGAEAELKTVAGYFSIVTTIFLRLIKMIIAPLV 68

Query: 54  ISSLVVGVASVGDLKKLGKLGGKTIIYFEIITTIAIVVGLLAANIFQPGAGVNMKSLEKT 113
            ++LV G+A +GD   LG++GG+ + +F   + +++ +GL+  N+FQPG G+N   L   
Sbjct: 69  FATLVAGIAHMGDTAALGRVGGRAVAWFICASLVSLTLGLILVNLFQPGVGLNFP-LPPV 127

Query: 114 DIQSYVDTTNEVQHHSMVETFVNIVPKNIFESLSTGDMLPIIFFSVMFGLGVAAIGEKGK 173
           D  S V    E    ++ + F ++ P +  E+++  ++L I+ FS+  G+ + A+GEK K
Sbjct: 128 DATSGV----EKAAFNLKDFFTHVFPASGIEAMAKNEILQIVIFSLFIGVAITAVGEKAK 183

Query: 174 PVLQFFQGTAEAMFYVTNQIMKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMLF 233
           P++   +     M  VTN +M+FAP  VFA +  T+++ G   +  L+  +   Y  M F
Sbjct: 184 PLVSAVEALVHVMLQVTNYVMRFAPIAVFAAVAGTLAERGPAIIGNLAYFMGTFYIAM-F 242

Query: 234 FIFAVLGGVAKLF-GINIFHIIKILKDELILAYSTASSETVLPRIMDKMEKFGCPKAITS 292
            ++A+L GV  L  G     +++ ++D L+LA+STASSE   PR ++ +++FG P  I S
Sbjct: 243 TLWALLIGVCYLIVGKRTGLLVRYIRDPLLLAFSTASSEAAYPRTLEALDRFGVPPRIAS 302

Query: 293 FVIPTGYSFNLDGSTLYQALAAIFIAQLYGIDMSVSQQISLLLVLMVTSKGIAGVPGVSF 352
           FV+P GYSFNLDGS +Y   A IFIAQ YGID+++ Q+I++LLVLM+TSKGIAGVP  S 
Sbjct: 303 FVLPLGYSFNLDGSMIYMTFATIFIAQAYGIDLTLGQEITMLLVLMITSKGIAGVPRASL 362

Query: 353 VVLLATLGTVGIPVEGLAFIAGIDRILDMARTAVNVIGNSLAAIIMSKWEG 403
           VV+ ATLG   IP  GL  I GID  LDM R+A NV+GN++A+ +++KWEG
Sbjct: 363 VVIAATLGFFDIPEAGLLLILGIDHFLDMGRSATNVVGNAVASAVVAKWEG 413


Lambda     K      H
   0.326    0.143    0.402 

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: 446
Number of extensions: 19
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: 421
Length of database: 455
Length adjustment: 32
Effective length of query: 389
Effective length of database: 423
Effective search space:   164547
Effective search space used:   164547
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 (21.6 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