Alignments for a candidate for xacD in Marinomonas arctica 328

GapMind for catabolism of small carbon sources

Alignments for a candidate for xacD in Marinomonas arctica 328

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 WP_111609172.1 DK187_RS20575 dihydroxy-acid dehydratase

Query= SwissProt::B5ZZ34
         (579 letters)



>NCBI__GCF_003259225.1:WP_111609172.1
          Length = 586

 Score =  944 bits (2440), Expect = 0.0
 Identities = 456/573 (79%), Positives = 510/573 (89%)

Query: 7   WPRKLRSQEWYGGTSRDVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLREL 66
           WPRKLRS EW+GGTSRD IYHR W+KNQG P DLFDGRPVIGI NTWS +TPCN HLREL
Sbjct: 14  WPRKLRSTEWFGGTSRDHIYHRSWMKNQGLPADLFDGRPVIGICNTWSQLTPCNAHLREL 73

Query: 67  AEKVKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDGCVLLVG 126
           A++VK G++EAGG PLE PVFS  E++ RPTAMMYRN+AA+ VEEA+R  P+DG VLL G
Sbjct: 74  ADRVKHGIYEAGGLPLEFPVFSVGESSLRPTAMMYRNMAAMDVEEALRANPLDGVVLLAG 133

Query: 127 CDKTTPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQAEF 186
           CDKTTP+LLMGA S D+P+IVV+GGPMLNGYFRGERVGSGT LW+ SE +KAG+MTQ +F
Sbjct: 134 CDKTTPALLMGACSVDIPAIVVSGGPMLNGYFRGERVGSGTALWQMSEDIKAGKMTQEDF 193

Query: 187 LEAEASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIVQ 246
           LEAE SMSRS+G CNTMGTASTMASMAEALGMALSGNAAIP VDSRR+VMA LTGRRIV 
Sbjct: 194 LEAEQSMSRSAGGCNTMGTASTMASMAEALGMALSGNAAIPAVDSRRRVMAHLTGRRIVD 253

Query: 247 MVKDDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRDV 306
           MVKDDLKPS+I+T+QAFENAIR N AIGGSTNAVIHLLAIAGRVG+DL+LDDWD+ G+++
Sbjct: 254 MVKDDLKPSDILTRQAFENAIRVNGAIGGSTNAVIHLLAIAGRVGVDLNLDDWDKLGQNI 313

Query: 307 PTIVNLMPSGKYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDVVNWNE 366
            TIVNLMPSGKYLMEEFFYAGGLPVV+K L EAG LHK+A+TVSGE++WDEVK+V NWN 
Sbjct: 314 ATIVNLMPSGKYLMEEFFYAGGLPVVIKHLAEAGKLHKNAITVSGESIWDEVKEVRNWNP 373

Query: 367 DVILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFEDIDDYKAKIN 426
           DVILP EKALT  GGIVVL+GNLAP GAVLKPSAAS HLL H+GRAVVFEDIDDYKAKIN
Sbjct: 374 DVILPVEKALTQKGGIVVLKGNLAPLGAVLKPSAASAHLLQHRGRAVVFEDIDDYKAKIN 433

Query: 427 DDNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRISDARMSGTAYGT 486
           D+ LDIDE+C+MV+KNCGPKGYPGMAEVGNMGLPPKVL+KGI DMVRISDARMSGTAYGT
Sbjct: 434 DEALDIDEHCVMVLKNCGPKGYPGMAEVGNMGLPPKVLRKGIKDMVRISDARMSGTAYGT 493

Query: 487 VVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLAEWQPNHDLPTSGY 546
           VVLHT+PEAA GGPLAV++NGDMIELDV NRRLH+DISDEE+A RLA W+ + + P SGY
Sbjct: 494 VVLHTTPEAAAGGPLAVIQNGDMIELDVENRRLHVDISDEEMATRLANWKSHLEAPKSGY 553

Query: 547 AFLHQQHVEGADTGADLDFLKGCRGNAVGKDSH 579
             L   HV+GADTGAD DFLKGCRG AV KDSH
Sbjct: 554 IKLFHDHVQGADTGADFDFLKGCRGAAVPKDSH 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: 1305
Number of extensions: 61
Number of successful extensions: 1
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 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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