GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Caulo:CCNA_00117
          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:

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