GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gluD in Herbaspirillum seropedicae SmR1

Align GluD aka CGL1953, component of Glutamate porter (characterized)
to candidate HSERO_RS17565 HSERO_RS17565 glutamate/aspartate ABC transporter permease GltJ

Query= TCDB::P48245
         (273 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS17565 HSERO_RS17565
           glutamate/aspartate ABC transporter permease GltJ
          Length = 241

 Score =  112 bits (280), Expect = 8e-30
 Identities = 74/229 (32%), Positives = 118/229 (51%), Gaps = 15/229 (6%)

Query: 12  KWTPFINS----QTWTTYILPGLWGTLKSAVFSVILALVMGTALGLGRISEIRILRWFCA 67
           +W+ F+ +    QT+  ++L GL  T+   + + ILALV+GT LG+ R    R L  F A
Sbjct: 6   QWSVFLQAPSTGQTYLDWLLSGLGVTVALGLSAWILALVLGTFLGILRTLPNRALSGFAA 65

Query: 68  VIIETFRAIPVLILMIFAYQMFAQYNIVPSSQLA---------FAAVVFGLTMYNGSVIA 118
             +E FR +P+L+ +   Y  FA   ++P              F   +  L M+  + + 
Sbjct: 66  CYVELFRNVPLLVQIFIWY--FAMPELLPWGDAVKALPPMTQQFVMAMLCLGMFTAARVC 123

Query: 119 EILRSGIASLPKGQKEAAIALGMSSRQTTWSILLPQAVAAMLPALISQMVIALKDSALGY 178
           E +RSGI SLP+GQK A +ALG++  QT   +LLP A+  +LP L S+ +   K+SA+  
Sbjct: 124 EQVRSGIESLPRGQKGAGLALGLTLGQTYLFVLLPMAMRIVLPPLTSEFLNIFKNSAVAS 183

Query: 179 QIGYIEVVRSGIQSASVNRNYLAALFVVALIMIVLNFSLTALASRIERQ 227
            IG +E+   G Q          A   V L  +++N  + +L   +ER+
Sbjct: 184 TIGLLELAAQGRQLVDYTAQPYEAFIAVTLAYMLINICVMSLMRILERK 232


Lambda     K      H
   0.323    0.136    0.395 

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: 181
Number of extensions: 12
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: 273
Length of database: 241
Length adjustment: 24
Effective length of query: 249
Effective length of database: 217
Effective search space:    54033
Effective search space used:    54033
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 47 (22.7 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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