GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagB in Shewanella loihica PV-4

Align Glucosamine-6-phosphate deaminase [isomerizing], alternative (EC 3.5.99.6) (characterized)
to candidate 5211430 Shew_3839 glucosamine--fructose-6-phosphate aminotransferase, isomerizing (RefSeq)

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



>FitnessBrowser__PV4:5211430
          Length = 609

 Score =  125 bits (315), Expect = 2e-33
 Identities = 95/312 (30%), Positives = 150/312 (48%), Gaps = 24/312 (7%)

Query: 66  VVTCARGSSDHAATFARYLIETKAGVLTSSAGPSVSSV--YDASPNLEGALYLAISQSGK 123
           ++ C  G+S HA   ARY +E  AGV   S    ++S   Y  S     +L + ISQSG+
Sbjct: 298 IIAC--GTSYHAGMAARYWLEDWAGV---SCNVEIASEFRYRKSHLFPNSLLVTISQSGE 352

Query: 124 SPDLLAAVKAAKAAGAHA-VALVNVVDSPLAALADEVIPLHAGPELSVAATKSYIAALVA 182
           + D LAA++ AK  G  A + + N   S L   +D    + AG E+ VA+TK++   L  
Sbjct: 353 TADTLAALRLAKEMGYKATLTICNAPGSSLVRESDMAYMMKAGAEIGVASTKAFTVQLAG 412

Query: 183 VTQLIAAWTED--------AELTAALQDLPTALAAAWTLDWSLA--VERLKTASNLYVLG 232
           +  L AA            AE+T +LQ +P  +  A  LD ++A   E      +   LG
Sbjct: 413 LLMLTAAVGRHNGMSPEMLAEITQSLQSMPAKVEQALGLDDAIAELAEDFADKHHALFLG 472

Query: 233 RGVGFGVALEAALKFKETCGLHAEAFSAAEVLHGPMALVKDGFPALVFAQNDESRASVDE 292
           RG  + +A+E ALK KE   +HAEA+++ E+ HGP+AL+    P +V A N+E    +  
Sbjct: 473 RGDQYPIAMEGALKLKEISYIHAEAYASGELKHGPLALIDADMPVIVVAPNNELLEKLKS 532

Query: 293 MAAGLRARGASVLIAGG------GGDAPDALPTLASHPVLEPILMIQSFYRMANALSVAR 346
               +RARG  + +           D    +P       + P++       ++  +++ +
Sbjct: 533 NVEEVRARGGLMYVFADKDAEFESDDTMKVIPVPHCDDYMAPLIYTIPLQLLSYHVALIK 592

Query: 347 GYDPDSPPHLNK 358
           G D D P +L K
Sbjct: 593 GTDVDQPRNLAK 604


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: 345
Number of extensions: 13
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: 609
Length adjustment: 33
Effective length of query: 330
Effective length of database: 576
Effective search space:   190080
Effective search space used:   190080
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