Alignments for a candidate for dgoD in Shewanella sp. ANA-3

GapMind for catabolism of small carbon sources

Alignments for a candidate for dgoD in Shewanella sp. ANA-3

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 7024896 Shewana3_2070 dihydroxy-acid dehydratase (RefSeq)

Query= SwissProt::B5ZZ34
         (579 letters)



>FitnessBrowser__ANA3:7024896
          Length = 586

 Score =  733 bits (1892), Expect = 0.0
 Identities = 366/573 (63%), Positives = 444/573 (77%), Gaps = 2/573 (0%)

Query: 8   PRKLRSQEWYGGTSRDVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLRELA 67
           P+ LRS  W+G   ++   +R W+KNQG P   F  +PVIGI NTWS++TPCNGHLRELA
Sbjct: 15  PKTLRSASWFGSDDKNGFMYRSWMKNQGIPEHHFQNKPVIGICNTWSELTPCNGHLRELA 74

Query: 68  EKVKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDGCVLLVGC 127
           ++VK G+ EAGG P+E PVFS  E+  RP+AM+ RNLAA+  EEAIRG P+DG VLLVGC
Sbjct: 75  QRVKNGIREAGGIPVEFPVFSNGESNLRPSAMLTRNLAAMDTEEAIRGNPIDGVVLLVGC 134

Query: 128 DKTTPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQAEFL 187
           DKTTP+LLMGAASCDLP+IVVTGGPMLNG  +G+ VGSGT +W+  +  KAG ++ A F+
Sbjct: 135 DKTTPALLMGAASCDLPTIVVTGGPMLNGKHKGKDVGSGTLVWELHQEYKAGNISLAAFM 194

Query: 188 EAEASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIVQM 247
            AEA MSRS+GTCNTMGTASTMA M E LG++L  NA IP VDSRR+V+A ++G RIV M
Sbjct: 195 NAEADMSRSTGTCNTMGTASTMACMVETLGVSLPHNATIPAVDSRRQVLAHMSGMRIVDM 254

Query: 248 VKDDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRDVP 307
           VK+DL  S+I+++ AF NAI+ NAAIGGSTNAVIHL AIAGR+G++LSLDDW R G  VP
Sbjct: 255 VKEDLTLSKILSRDAFINAIKVNAAIGGSTNAVIHLKAIAGRIGVELSLDDW-RHGYTVP 313

Query: 308 TIVNLMPSGKYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDVVNWNED 367
           TIVNL PSG+YLME+F+YAGGLP VL++L E  LL K+ LTV+  ++WD VK+   +N++
Sbjct: 314 TIVNLKPSGQYLMEDFYYAGGLPAVLRQLFEHDLLSKNTLTVNAASLWDNVKEAPCYNQE 373

Query: 368 VILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFEDIDDYKAKIND 427
           VI+  E  L  +GGI VLRGNLAP+GAV+KPSAAS HL+ H+G+AVVFE  DDY A+I D
Sbjct: 374 VIMSLENPLVENGGIRVLRGNLAPRGAVIKPSAASAHLMQHRGKAVVFESFDDYNARIGD 433

Query: 428 DNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRISDARMSGTAYGTV 487
             LDIDEN IMV+KNCGPKGYPGMAEVGNMGLPPK+LKKGI DMVRISDARMSGTA+GTV
Sbjct: 434 PELDIDENSIMVLKNCGPKGYPGMAEVGNMGLPPKLLKKGIKDMVRISDARMSGTAFGTV 493

Query: 488 VLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLAEWQPNHDLPTS-GY 546
           VLH +PEA   GPLA V+NGDMI LD     L L+ISD+EL  RLA+      +P + GY
Sbjct: 494 VLHVAPEAQALGPLAAVQNGDMIALDTYAGTLQLEISDQELQARLAKLATVKSIPVNGGY 553

Query: 547 AFLHQQHVEGADTGADLDFLKGCRGNAVGKDSH 579
             L ++HV  AD G D DFL GCRG  +   SH
Sbjct: 554 LSLFKEHVLQADEGCDFDFLVGCRGAEIPAHSH 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: 1083
Number of extensions: 54
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: 586
Length adjustment: 36
Effective length of query: 543
Effective length of database: 550
Effective search space:   298650
Effective search space used:   298650
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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources