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 Pf1N1B4_4274 5-keto-2-deoxygluconokinase (EC 2.7.1.92) / uncharacterized domain
Query= reanno::pseudo3_N2E3:AO353_21335 (645 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4274 Length = 645 Score = 1233 bits (3189), Expect = 0.0 Identities = 612/645 (94%), Positives = 632/645 (97%) Query: 1 MGQTRFASGRQLDLICLGRLGVDLYAQQVGARLEDVSSFAKYLGGSSANIAFGTARLGLK 60 MGQTRFASGRQLDLICLGRLGVDLYAQQVGARLEDVSSFAKYLGGSSANIAFGTARLGLK Sbjct: 1 MGQTRFASGRQLDLICLGRLGVDLYAQQVGARLEDVSSFAKYLGGSSANIAFGTARLGLK 60 Query: 61 SAMLSRVGDDHMGRFLVESLAREGCDVSGIKVDPERLTAMVLLGLKDRETFPLVFYRENC 120 SAMLSRVGDDHMGRFLVESL REGCDVSGIKVDPERLTAMVLLGLKDRETFPLVFYRENC Sbjct: 61 SAMLSRVGDDHMGRFLVESLTREGCDVSGIKVDPERLTAMVLLGLKDRETFPLVFYRENC 120 Query: 121 ADMALRAEDISEAFIASSKALLITGTHFSTDGVYKASIQALEYAEKHNVKRILDIDYRPV 180 ADMALRAEDI+EAFIASSKALLITGTHFSTDGVYKASIQAL+YAEKHNVKR+LDIDYRPV Sbjct: 121 ADMALRAEDINEAFIASSKALLITGTHFSTDGVYKASIQALDYAEKHNVKRVLDIDYRPV 180 Query: 181 LWGLAGKADGETRFVADQQVSQHVQKILPRFDLIVGTEEEFLIAGGSEDLLSALRNVRRL 240 LWGLAGKADGETRFVADQ VSQHVQKILPRFDLIVGTEEEFLIAGGSEDLL+AL+NVRRL Sbjct: 181 LWGLAGKADGETRFVADQNVSQHVQKILPRFDLIVGTEEEFLIAGGSEDLLTALQNVRRL 240 Query: 241 TAATLVVKLGPQGCTVIHGVIPVRLEDGAIYPGVRVEVLNVLGAGDAFMSGFLSGWLEDA 300 +AATLVVKLGPQGCTVIHG IP RLEDGAIYPGVRVEVLNVLGAGDAFMSGFLSGWLEDA Sbjct: 241 SAATLVVKLGPQGCTVIHGAIPARLEDGAIYPGVRVEVLNVLGAGDAFMSGFLSGWLEDA 300 Query: 301 SDERCCQLANACGGLVVSRHACAPAMPTRAELDYLFNSPVPITRPDQDAVLQRLHQVSVP 360 SDERCCQLANACG LVVSRHACAPAMPTRAELDYLFNSPVPITRPDQDAVLQRLHQVSVP Sbjct: 301 SDERCCQLANACGALVVSRHACAPAMPTRAELDYLFNSPVPITRPDQDAVLQRLHQVSVP 360 Query: 361 RKTWKQLFIFAFDHRGQLVELAQKGGRELSSIGELKQLFIKAVERVEADLRRQGIEADVG 420 RK WKQLFIFAFDHRGQLVELA KGGR+LSSIGELKQLFIKAVERVEADLR QG++ADVG Sbjct: 361 RKQWKQLFIFAFDHRGQLVELAHKGGRDLSSIGELKQLFIKAVERVEADLREQGVDADVG 420 Query: 421 LLADQRFGQDSLNAATGRGWWVARPVEVQGSRPLAFEHGRSIGSNLIAWPQEQIIKCLVQ 480 LLADQRFGQDSLNAATGRGWWVARPVEVQGSRPLAFEHGRSIGSNLIAWPQEQIIKCLVQ Sbjct: 421 LLADQRFGQDSLNAATGRGWWVARPVEVQGSRPLAFEHGRSIGSNLIAWPQEQIIKCLVQ 480 Query: 481 FHPDDEPLLRLEQEAQIKGLYQAAQVSGHELLLEIIPPKDHPSAHPDVLYRAIKRLYNLG 540 FHPDDEPLLRLEQEAQIKGLYQA+QVSGHELLLEIIPPKDHPS HPDVLYRA+KRLY+LG Sbjct: 481 FHPDDEPLLRLEQEAQIKGLYQASQVSGHELLLEIIPPKDHPSQHPDVLYRALKRLYSLG 540 Query: 541 IFPAWWKIEAQSSEEWKQLDDLIQERDPYCRGVVLLGLNAPAATLAEGFAQASQSKTCRG 600 I+PAWWKIEAQS+EEWKQLD+LIQERDPYCRGVVLLGLNAPAA LAEGF QASQS+TCRG Sbjct: 541 IYPAWWKIEAQSAEEWKQLDELIQERDPYCRGVVLLGLNAPAAALAEGFQQASQSQTCRG 600 Query: 601 FAVGRTIFQEPSRAWLAGEIDDEALIQRVQGTFVELINAWRTARA 645 FAVGRTIFQEPSRAW+AGEIDDE LI++VQGTFVELI+AW TARA Sbjct: 601 FAVGRTIFQEPSRAWMAGEIDDETLIRQVQGTFVELIDAWCTARA 645 Lambda K H 0.321 0.138 0.412 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: 1415 Number of extensions: 37 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: 645 Length of database: 645 Length adjustment: 38 Effective length of query: 607 Effective length of database: 607 Effective search space: 368449 Effective search space used: 368449 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