GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Smeli:SMc02877 SMc02877 hypothetical protein
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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