GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagB in Desulfovibrio vulgaris Miyazaki F

Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate 8500969 DvMF_1706 glucosamine/fructose-6-phosphate aminotransferase, isomerizing (RefSeq)

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



>FitnessBrowser__Miya:8500969
          Length = 607

 Score =  128 bits (322), Expect = 4e-34
 Identities = 111/344 (32%), Positives = 162/344 (47%), Gaps = 34/344 (9%)

Query: 36  AARVAAVQLTANAPKIQALAQRLRANPPRVVVTCARGSSDHAATFARYLIETKAGVLTSS 95
           A RV   ++    P++ AL    R +    +V C  G+S HA  + ++L+E+ A V  + 
Sbjct: 272 AGRVDWNRMEVTLPELAALPVPKRLH----IVAC--GTSYHAGMWGKHLLESWARVPVNV 325

Query: 96  AGPSVSSVYDASPNLEGALYLAISQSGKSPDLLAAVKAAKAAGAHAVALVNVVDSPLAAL 155
              S     D   +    + L ISQSG++ D LAA++ A+  G     L NVV S +A  
Sbjct: 326 EIASEFRYRDIILD-PADMVLVISQSGETADTLAALRIAREHGVKVAGLCNVVGSSIARE 384

Query: 156 ADEVIPLHAGPELSVAATKSYIAALVAVTQLIAAW---------TEDAELTAALQDLPTA 206
           AD VI   AGPE+SVA+TK+  + +V +T +   W         T  A +   L+ LP  
Sbjct: 385 ADAVIYTQAGPEISVASTKAMCSQMVLLTLMALHWGRNTGALSETVRANVLQTLRKLPGQ 444

Query: 207 LAA---AWTLDWSLAVERLKTASNLYVLGRGVGFGVALEAALKFKETCGLHAEAFSAAEV 263
           L     A   +  +       A + + LGRG  F +ALE ALK KE   +HAE +++ E+
Sbjct: 445 LETVLPAMRDEAQVLARTYSKAKSFFYLGRGHCFPLALEGALKLKEISYIHAEGYASGEM 504

Query: 264 LHGPMALVKDGFPALVFAQNDESRASVDEMAAGLRARGASVLIAGGGG---------DAP 314
            HGP+AL+   FP    A NDE    V      ++AR   ++     G           P
Sbjct: 505 KHGPIALIDPDFPTFALALNDELFPKVKSNIEEVQARRGKIIALTNPGVELKVDHPWSIP 564

Query: 315 DALPTLASHPVLEPILMIQSFYRMANALSVARGYDPDSPPHLNK 358
           DA   +A+  VL P L + S Y  A+ L    G D D P +L K
Sbjct: 565 DAWGPMAAFLVL-PALQLFS-YEAADYL----GKDVDQPRNLAK 602


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: 410
Number of extensions: 21
Number of successful extensions: 3
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: 607
Length adjustment: 33
Effective length of query: 330
Effective length of database: 574
Effective search space:   189420
Effective search space used:   189420
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