GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagB in Sinorhizobium meliloti 1021

Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate SMc02877 SMc02877 hypothetical protein

Query= reanno::Phaeo:GFF2746
         (342 letters)



>FitnessBrowser__Smeli:SMc02877
          Length = 340

 Score =  354 bits (908), Expect = e-102
 Identities = 185/337 (54%), Positives = 241/337 (71%)

Query: 5   TKMRREIDEIPTAVDRLLSHGRVEIEAVADAARALDPNVMVTVARGSSDHVCTYLKYASE 64
           T MRREIDEIP A  RLL      +     A RA DP  +VT+ARGSSDH   +LKYA E
Sbjct: 3   TNMRREIDEIPEAAARLLERSATRLAQAGAALRAKDPAFLVTIARGSSDHAALFLKYAIE 62

Query: 65  IMLGVPVASVGPSVASIYKAPLRLKGALSLAVSQSGKSPDIVSMAGSARKDGALSVALTN 124
           +  G PVAS+GPS+ASIY A L+L GA ++A+SQSGKSPDIV+MA +A + GA+S+ALTN
Sbjct: 63  LTTGRPVASLGPSLASIYGADLKLGGAAAIAISQSGKSPDIVAMAEAATRAGAVSIALTN 122

Query: 125 DAASPLAAAADHTLDIHAGPELSVAATKTFVTSAVAGLWLLAQWDRNQAVLAALHALPEQ 184
              SP+A A  H LDI AGPE++VAATK++V S VAGL +L +W  +  +  A+  LP Q
Sbjct: 123 TLPSPIAEACTHPLDILAGPEIAVAATKSYVNSIVAGLAVLGEWTGDATLKHAVADLPNQ 182

Query: 185 LDRACRIDWPEVRDAIGARSSLFTLGRGQALAVSNEAALKFKETCQLHAESYSSAEVLHG 244
           L +A ++DW +    +    SL+ LGRG ALA+++EAALKFKET  +HAE+YS+AEVLHG
Sbjct: 183 LAKAVKLDWQDFAGDLAEAESLYVLGRGPALAIASEAALKFKETSGMHAEAYSAAEVLHG 242

Query: 245 PVSIVEEGFPVLGFAAADAAEGALAGIADQIAAKGAQVFATTDKVTAARRVDHVRTDHAL 304
           PV++V   FPVL  AA DAAE ++A IAD ++AKGA V  T+ +   A+R+  V T H L
Sbjct: 243 PVALVGHRFPVLVLAARDAAEASVADIADGMSAKGAVVHVTSARAGKAKRLPFVETGHPL 302

Query: 305 TDPISLIVSFYAMVEAFAASRGIDPDAPRHLKKVTET 341
           TD ++LI+ FY  VEA++ SRG++PDAP +LKKVTET
Sbjct: 303 TDALALILPFYGFVEAWSRSRGLNPDAPENLKKVTET 339


Lambda     K      H
   0.317    0.129    0.364 

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: 292
Number of extensions: 9
Number of successful extensions: 1
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: 342
Length of database: 340
Length adjustment: 29
Effective length of query: 313
Effective length of database: 311
Effective search space:    97343
Effective search space used:    97343
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 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