GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dgoD in Herbaspirillum seropedicae SmR1

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 HSERO_RS22480 HSERO_RS22480 dihydroxy-acid dehydratase

Query= SwissProt::B5ZZ34
         (579 letters)



>FitnessBrowser__HerbieS:HSERO_RS22480
          Length = 594

 Score =  448 bits (1153), Expect = e-130
 Identities = 245/587 (41%), Positives = 363/587 (61%), Gaps = 15/587 (2%)

Query: 1   MKKKAEWPRKLRSQEWYGGTSR---DVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMT 57
           M K    PR+ RSQ+W+          +Y   ++       +L  GRP+IGI  + SD++
Sbjct: 1   MNKPNATPRRFRSQDWFDNPDHIDMTALYLERFMNYGITAEELRSGRPIIGIAQSGSDIS 60

Query: 58  PCNGHLRELAEKVKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQP 117
           PCN    ELA++V+ G+ +AGG P+E P+    EN  RPTA + RNLA L + E + G P
Sbjct: 61  PCNRIHLELAKRVRDGIRDAGGIPMEFPLHPIFENCRRPTAAIDRNLAYLGLVEILHGYP 120

Query: 118 MDGCVLLVGCDKTTPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVK 177
           +D  VL  GCDKTTPS +M AA+ D+P+IV++GGPML+G+  GE VGSG+ +WK  +++ 
Sbjct: 121 IDAVVLTTGCDKTTPSQIMAAATVDIPAIVLSGGPMLDGWMDGELVGSGSAIWKGRKLLS 180

Query: 178 AGEMTQAEFLEAEASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMA 237
           AG +   +FLE  A+ + SSG CNTMGTASTM +MAEALGM+L+G +AIP     R  MA
Sbjct: 181 AGSIDNEKFLEIAAASAPSSGHCNTMGTASTMNAMAEALGMSLTGCSAIPAPYRERGQMA 240

Query: 238 QLTGRRIVQMVKDDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLD 297
             TGRRIV M  +DL+PS I+T+ AF +AI  NAAIGGSTNA  H++A+A   G++L  +
Sbjct: 241 YETGRRIVGMAYEDLRPSAILTRDAFLDAIVVNAAIGGSTNAQPHIMAMARHAGVELQSE 300

Query: 298 DWDRCGRDVPTIVNLMPSGKYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDE 357
           DW + G DVP ++N+ P+GKYL E F  AGG+P ++  L +AG L  + +T +G+T+ + 
Sbjct: 301 DWMKYGYDVPLLLNMQPAGKYLGERFHRAGGVPAIMWELQQAGKLRAERITATGKTMAEN 360

Query: 358 VKDVVNWNEDVILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLL----------- 406
           ++   + + ++I P    L    G +VL+GNL    A++K S  S               
Sbjct: 361 LQGRASNDREMIYPFAAPLRERAGFLVLKGNLF-DFAIMKTSVISETFRERYLSTPGQEN 419

Query: 407 VHKGRAVVFEDIDDYKAKINDDNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKK 466
           + + RAVVF+  DDY A+IND  L IDEN ++ ++  GP G+PG AEV NM  P  ++K+
Sbjct: 420 IFECRAVVFDGSDDYHARINDPALKIDENTLLAIRGAGPVGWPGSAEVVNMQPPDALIKR 479

Query: 467 GILDMVRISDARMSGTAYGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDE 526
           G+  +  + D R SGT+    +L+ SPE+AVGG LA +++GD + +D+     ++ +S+E
Sbjct: 480 GVSTLPTLGDGRQSGTSDSPSILNASPESAVGGGLAYLRDGDRVRIDLNTGECNMLVSEE 539

Query: 527 ELARRLAEWQPNHDLPTSGYAFLHQQHVEGADTGADLDFLKGCRGNA 573
           ELARR +E  P      + +  +++  V   +TGA ++     +G A
Sbjct: 540 ELARRKSEGIPPVPPSQTPWQEIYRSTVGQLETGACMELALKYQGVA 586


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: 960
Number of extensions: 48
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: 579
Length of database: 594
Length adjustment: 37
Effective length of query: 542
Effective length of database: 557
Effective search space:   301894
Effective search space used:   301894
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.

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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