Align Ribulokinase (EC 2.7.1.16) (characterized)
to candidate Echvi_4514 Echvi_4514 Ribulose kinase
Query= reanno::Cola:Echvi_0515 (562 letters) >FitnessBrowser__Cola:Echvi_4514 Length = 557 Score = 603 bits (1556), Expect = e-177 Identities = 290/552 (52%), Positives = 398/552 (72%), Gaps = 2/552 (0%) Query: 1 MNDKFVIGLDYGSDSVRAVIVNTGNGEVKGSHVFWYPRWKAGKYCDPVNNQFRQHPLDHL 60 M+ FVIG+D+G+DSVR+++V+T +G++ S V+ YPRW YCD ++QFRQHPLDHL Sbjct: 1 MSKNFVIGVDFGTDSVRSILVDTLDGKIVKSAVYRYPRWSKKLYCDAGSHQFRQHPLDHL 60 Query: 61 EGLEETIREVIKESGVPADQIKGICVDTTGSSPMAVDQQGKPLALSPEFAENPNAMMVLW 120 EGLE T+ +I++SG+ D +KGI V TTGSSP+ VD+ G L++S F+ NPNAM+VLW Sbjct: 61 EGLEHTVSAIIRDSGIDPDSVKGIGVATTGSSPIPVDENGDALSMSSRFSNNPNAMVVLW 120 Query: 121 KDHTAIKEADEINELARTWGGEDYTKYEGGIYSSEWFWAKILHVIREDDAVAQAAYSWME 180 KDHTA+ EA+EI + A+ G DYT + GG YSSEWFWAKIL V ++D VA+ +WME Sbjct: 121 KDHTAVAEAEEITKAAKN-GEVDYTAFSGGSYSSEWFWAKILSVYKKDPGVARNTCTWME 179 Query: 181 HCDVITAELIGADNPLDVKRSRCAAGHKALWHESWDGLPPKEFLSKLDPRLADLRDRLYT 240 HCD I +L G + PL++KRSR AAGHKA+W++ W GLPP F + P L LR+ LY Sbjct: 180 HCDFIVGQLTG-ERPLNLKRSRTAAGHKAMWNKKWSGLPPASFWGGISPELGSLRETLYE 238 Query: 241 ETFTSDLPAGNLSAEWAKKLGLSTDTVIAVGTFDAHAGAVGGEVTENTLVKVMGTSTCDI 300 +TF AG+L ++WA+KLGLS DT +AVGT DAHAGAVG ++ NTLVKV+GTSTCDI Sbjct: 239 QTFHGSEKAGHLCSKWAEKLGLSADTAVAVGTLDAHAGAVGAGISPNTLVKVVGTSTCDI 298 Query: 301 MVATHEAIGDNLVKGICGQVDGSVIPGTVGLEAGQSGFGDVLAWFKHLVVKPTAALIRAS 360 +V + + ++GICGQV+ +V+PGT+GLEAGQ+GFGDVLAWF +V+ P+ +I S Sbjct: 299 LVGSPTDPELDPIEGICGQVEDAVLPGTIGLEAGQAGFGDVLAWFAEVVLGPSRQIIHRS 358 Query: 361 NVLDEEKKEALIHEIDSQLLIKLSEEAIQIPLSETAPVALDWVNGRRTPDANQALKGAVM 420 LD KE +I E++ +L +LS EA+++ ALDW+NGRR+P A + LKGA + Sbjct: 359 TQLDAVIKETIIEELEHSILDELSREALELAPCLNGASALDWINGRRSPFAKETLKGAFL 418 Query: 421 GLNMGTDAARVFKALVESICFGSKKIVDRFREEGVAIDTVIGMGGVAKKSKLVMQTMADV 480 L+MGT A+ +F+A+VE++CFGSKKI+D +G+ ++ +I +GGVA KS LVMQTMAD+ Sbjct: 419 NLHMGTQASHMFRAMVEALCFGSKKIIDHLEGKGLTVEEIIAIGGVANKSPLVMQTMADI 478 Query: 481 LNMPIKIATSDQAPALGAAMYASVAAGIHPTTEAAIAAMTNGFDKVYEPIPENVEVYKAL 540 + PIKIA S +APALGAA++A+VA+ ++P+ + A+A M F KVY P ++ +VY Sbjct: 479 IGKPIKIAASKEAPALGAAIHAAVASKVYPSMDQAVAKMVPAFKKVYSPDLQHQQVYVEK 538 Query: 541 YAKYAEFGAFVE 552 Y Y G VE Sbjct: 539 YKMYEREGEVVE 550 Lambda K H 0.316 0.133 0.398 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: 956 Number of extensions: 50 Number of successful extensions: 5 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: 562 Length of database: 557 Length adjustment: 36 Effective length of query: 526 Effective length of database: 521 Effective search space: 274046 Effective search space used: 274046 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 (21.6 bits) S2: 53 (25.0 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