GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nagB in Caulobacter crescentus NA1000

Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate CCNA_00117 CCNA_00117 glucosamine-fructose-6-phosphate aminotransferase, isomerizing

Query= reanno::Caulo:CCNA_00453
         (363 letters)



>lcl|FitnessBrowser__Caulo:CCNA_00117 CCNA_00117
           glucosamine-fructose-6-phosphate aminotransferase,
           isomerizing
          Length = 606

 Score =  128 bits (321), Expect = 5e-34
 Identities = 104/313 (33%), Positives = 154/313 (49%), Gaps = 25/313 (7%)

Query: 66  VVTCARGSSDHAATFARYLIETKAGVLTSSAGPSVSSVYDASPNLE-GALYLAISQSGKS 124
           +V C  G+S  A    +YLIE  A +         S     +P L  G+L +A+SQSG++
Sbjct: 294 IVAC--GTSYIAGVIGKYLIEQLADLPVDVE--IASEFRYRTPALRPGSLVVAMSQSGET 349

Query: 125 PDLLAAVKAAKAAGAHAVALVNVVDSPLAALADEVIPLHAGPELSVAATKSYIAAL-VAV 183
            D LAA++  KA G  +  +VN  +S +A   D V P+H GPE+ VA+TK++ A + V +
Sbjct: 350 ADTLAALRYCKAKGMKSAVVVNAQESTMAREVDVVWPIHCGPEIGVASTKAFTAQVSVMI 409

Query: 184 TQLIAA--------WTEDAELTAALQDLPTALAAAWTLD---WSLAVERLKTASNLYVLG 232
              IAA          E+  L   L + P  +A A  L+     +A +  K    LY LG
Sbjct: 410 ALAIAAAKARGTIDAAEEQRLVKVLLEAPRLIAEAIGLEDAIKEIAADVAKARDVLY-LG 468

Query: 233 RGVGFGVALEAALKFKETCGLHAEAFSAAEVLHGPMALVKDGFPALVFAQNDESRASVDE 292
           RG    +ALE ALK KE   +HAE ++A E+ HGP+ALV D  P ++ A  D        
Sbjct: 469 RGPMSALALEGALKLKEISYIHAEGYAAGELKHGPIALVDDQTPIVILAPYDSYFEKSAS 528

Query: 293 MAAGLRARGASVLI---AGGGGDAPDALPTL----ASHPVLEPILMIQSFYRMANALSVA 345
             + + ARG  V+      G   AP     +    AS P++  ++M      +A  ++V 
Sbjct: 529 NMSEVMARGGQVIFITDTEGVKHAPAGAKVVVTAPASDPLVSTLVMSAPIQLLAYHVAVV 588

Query: 346 RGYDPDSPPHLNK 358
           +G D D P +L K
Sbjct: 589 KGADVDQPRNLAK 601


Lambda     K      H
   0.315    0.128    0.360 

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: 416
Number of extensions: 20
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: 363
Length of database: 606
Length adjustment: 33
Effective length of query: 330
Effective length of database: 573
Effective search space:   189090
Effective search space used:   189090
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 (21.6 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 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