GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dgoD in Sinorhizobium meliloti 1021

Align L-arabinonate dehydratase; ArDHT; D-fuconate dehydratase; Galactonate dehydratase; L-arabonate dehydratase; EC 4.2.1.25; EC 4.2.1.67; EC 4.2.1.6 (characterized)
to candidate SMc04144 SMc04144 dihydroxy-acid dehydratase

Query= SwissProt::B5ZZ34
         (579 letters)



>FitnessBrowser__Smeli:SMc04144
          Length = 574

 Score =  563 bits (1452), Expect = e-165
 Identities = 277/560 (49%), Positives = 381/560 (68%), Gaps = 3/560 (0%)

Query: 8   PRKLRSQEWYGGTSRDVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLRELA 67
           P + RS  W+G        HR  L   GY H     +PVI I+NTWSD+ PC+ HLR  A
Sbjct: 7   PEEFRSFRWFGVKDLRAFGHRSRLYQMGYDHAELANKPVIAIINTWSDINPCHAHLRARA 66

Query: 68  EKVKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDGCVLLVGC 127
           E+VK GVW+AGGFP+E+P  S +E   +PT M+YRN  A+ VEE IR  P+DG VLL GC
Sbjct: 67  EEVKRGVWQAGGFPIELPAMSLAETYVKPTTMLYRNFLAMEVEELIRSHPVDGVVLLAGC 126

Query: 128 DKTTPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQAEFL 187
           DKTTP  +MGA   DLP+I V  GPML G +RG  +GSG+ +WK+    +AG +T+ E+ 
Sbjct: 127 DKTTPGTIMGAIQVDLPTIFVPAGPMLRGNYRGRMLGSGSDVWKYWAEKEAGRVTENEWS 186

Query: 188 EAEASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIVQM 247
           E E  ++RS GTC TMGTASTM ++A+ LG++L G +AIP  D+    MA L+G RIV+M
Sbjct: 187 EMERGIARSFGTCMTMGTASTMTALADTLGLSLPGASAIPAADAGHARMAALSGARIVEM 246

Query: 248 VKDDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRDVP 307
           V +DLKPS+I+T +AFENA+  + A+ GSTNA+IHL+AIA R G+ L+LDD+DR   +VP
Sbjct: 247 VFEDLKPSDILTAKAFENALAVHMAMAGSTNAMIHLIAIARRCGVPLTLDDFDRVSAEVP 306

Query: 308 TIVNLMPSGKYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDVVNWNED 367
            + N+ P+G++LME+F+YAGGL  + K+L    LLH     V G T+   + +      +
Sbjct: 307 VLCNIRPTGEFLMEDFYYAGGLIALWKQL--KPLLHTGERNVIG-TIGGALDEAEVHLPE 363

Query: 368 VILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFEDIDDYKAKIND 427
           VI P ++ + + GG  +L+GNLAP+G V+KP+AA P LL H+G A+VF+D D     +ND
Sbjct: 364 VIRPLDRPVAARGGTAILKGNLAPQGCVMKPAAADPALLQHRGPALVFDDYDAMMKAVND 423

Query: 428 DNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRISDARMSGTAYGTV 487
           D+LD+  + +M+++N GP G PGM E G + +P K+LK+G+ DMVRISDARMSGT+YG  
Sbjct: 424 DDLDVTADTVMILRNAGPVGGPGMPEWGMLPIPRKLLKEGVRDMVRISDARMSGTSYGAC 483

Query: 488 VLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLAEWQPNHDLPTSGYA 547
           +LH +PEA VGGPLA V+NGD+I LDV  R + L++   E+ RRLAEW+P     + GY 
Sbjct: 484 ILHVAPEAYVGGPLAAVRNGDIIALDVARRTITLEVDQAEIERRLAEWRPPERDYSRGYL 543

Query: 548 FLHQQHVEGADTGADLDFLK 567
            +H +H++ A  G D  FL+
Sbjct: 544 KMHAEHIQQAPEGCDFTFLQ 563


Lambda     K      H
   0.318    0.135    0.408 

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: 1016
Number of extensions: 42
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: 579
Length of database: 574
Length adjustment: 36
Effective length of query: 543
Effective length of database: 538
Effective search space:   292134
Effective search space used:   292134
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: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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