Align 5-dehydro-2-deoxygluconokinase (EC 2.7.1.92); possible 5-dehydro-2-deoxyphosphogluconate aldolase DUF2090 (EC 4.1.2.29) (characterized)
to candidate H281DRAFT_04459 H281DRAFT_04459 5-dehydro-2-deoxygluconokinase
Query= reanno::BFirm:BPHYT_RS13910 (681 letters) >FitnessBrowser__Burk376:H281DRAFT_04459 Length = 682 Score = 1258 bits (3254), Expect = 0.0 Identities = 626/683 (91%), Positives = 651/683 (95%), Gaps = 3/683 (0%) Query: 1 MDQSITSSGVTSASAP--ATGSRFAPGRSRDIVCLGRLAVDLYAQQVGARLEDVSSFAKY 58 M QS T SG T A P A GSRFAPGRSRDIVCLGRLAVDLYAQQVGARLEDVSSFAKY Sbjct: 1 MAQSSTFSG-TPAQQPGGAAGSRFAPGRSRDIVCLGRLAVDLYAQQVGARLEDVSSFAKY 59 Query: 59 LGGSSANIAFGCARLGLASSMLARVGNDHMGRFLTETLTKEGCDVSHVRIDQERLTALVL 118 LGGSSANIAFGCARLGLAS+MLARVGNDHMGRFLTETLTKEGCDVSHVR+D ERLTALVL Sbjct: 60 LGGSSANIAFGCARLGLASAMLARVGNDHMGRFLTETLTKEGCDVSHVRVDPERLTALVL 119 Query: 119 LGLKDRDTFPLIFYRENCADMAVDEADFDEAYIASSKALLITGTHFSTEQVNRTSRRALD 178 LGLKDRDTFPLIFYRENCADMAVDEADFDEA+IASSKALLITGTHFSTEQVNRTSRRALD Sbjct: 120 LGLKDRDTFPLIFYRENCADMAVDEADFDEAFIASSKALLITGTHFSTEQVNRTSRRALD 179 Query: 179 YARRNQVRTVLDIDYRPVLWGLTGKADGETRFVASEGVTAHLQRILPLFDLVIGTEEEFR 238 YARRNQVRTVLDIDYRPVLWGLTGKADGETRFVASEGVTAHLQRILPLFDLVIGTEEEFR Sbjct: 180 YARRNQVRTVLDIDYRPVLWGLTGKADGETRFVASEGVTAHLQRILPLFDLVIGTEEEFR 239 Query: 239 IAGGKTELVDALAMVRAVTPATLVLKRGPMGCQIIDGAVPASLDDLPIHGGVEVEVLNVL 298 IAGGK++L+DALAMVRAVTPATLVLKRGPMGCQIIDG VPASLDD P+HGGVEVEVLNVL Sbjct: 240 IAGGKSDLLDALAMVRAVTPATLVLKRGPMGCQIIDGEVPASLDDTPVHGGVEVEVLNVL 299 Query: 299 GAGDAFASGFLSGWLRDQPLEACARIANASGALVVSRHGCAPAMPTPAELDYFLREAKAD 358 GAGDAFASGFLSGWLRDQPL+ACAR ANASGALVVSRH CAPAMPTPAELDYFLREAKAD Sbjct: 300 GAGDAFASGFLSGWLRDQPLDACARAANASGALVVSRHACAPAMPTPAELDYFLREAKAD 359 Query: 359 PQRMRRPDRDATLARLHRVSPARKQWDEVLGFAFDHRNQFFELAQQTGADDARIARLKGL 418 P+RMRRPDRDATLARLHRV+PARKQWDEVLGFAFDHRNQFFELAQQ+GA +ARIA+LKGL Sbjct: 360 PERMRRPDRDATLARLHRVTPARKQWDEVLGFAFDHRNQFFELAQQSGASEARIAQLKGL 419 Query: 419 FVEAVAQTESALGLQNRIGVLIDDRYGQDALNAATGRGWWIGRPVELPGSVPLVFDHGRS 478 FV+AVAQTESALGLQ RIGVLID RYGQDALNAATGRGWWIGRPVELPGSVPLVFDHGRS Sbjct: 420 FVDAVAQTESALGLQGRIGVLIDSRYGQDALNAATGRGWWIGRPVELPGSVPLVFDHGRS 479 Query: 479 IGTTLIPWPQEHIVKCLVQFHPDEPIEQRLEQEAQLRALYDATQASGHELLLEVIPPKHA 538 +GTTL+ WPQEH+ KCLVQFHPDEP+EQRLEQEAQLRALYDATQASGHELLLEVIPPKHA Sbjct: 480 VGTTLVSWPQEHVAKCLVQFHPDEPVEQRLEQEAQLRALYDATQASGHELLLEVIPPKHA 539 Query: 539 HLPQAPDTVYRALKRLYNIGIYPEWWKLEPMDAAQWRNVDALIAERDPYCRGVVLLGLSA 598 +LPQ PD VYRALKRLYNIGIYPEWWKLEPMDAAQWRN+DALIAERDPYCRGVVLLGLSA Sbjct: 540 NLPQGPDIVYRALKRLYNIGIYPEWWKLEPMDAAQWRNIDALIAERDPYCRGVVLLGLSA 599 Query: 599 AVEQLDEGFRAAAQSATCRGFTVGRTIFHEPSHAWLAGEIGDDELIGRVRRTFETLIASW 658 VEQL+EGFRAAA+S+TCRGFTVGRTIFHEPSHAWLAGEIGDDELI RVRRTFETLIASW Sbjct: 600 GVEQLNEGFRAAARSSTCRGFTVGRTIFHEPSHAWLAGEIGDDELIARVRRTFETLIASW 659 Query: 659 RATRGASAAQSSAPKPVHQEQAA 681 RA R +AA+ A VHQEQAA Sbjct: 660 RAARDTAAAERGASNRVHQEQAA 682 Lambda K H 0.321 0.136 0.409 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: 1527 Number of extensions: 41 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: 681 Length of database: 682 Length adjustment: 39 Effective length of query: 642 Effective length of database: 643 Effective search space: 412806 Effective search space used: 412806 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 54 (25.4 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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:
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