Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_073038485.1 BUB04_RS08085 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_900129305.1:WP_073038485.1 Length = 398 Score = 387 bits (993), Expect = e-112 Identities = 207/393 (52%), Positives = 267/393 (67%), Gaps = 7/393 (1%) Query: 5 TIRDVDLKGKRVIMRVDFNVPV--KDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGR 62 T+ VD+ KRV +RVDFNVP+ KDG V DDTRIRA LP+++ L+ G K +L SHLGR Sbjct: 3 TLDHVDVSAKRVFLRVDFNVPLDKKDGTVADDTRIRAILPSLRKVLDGGGKAVLASHLGR 62 Query: 63 PKGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPG 122 PKG+ PE SLAPVA+ LS +LG +V P VG V+K V+EL+ G VLLLEN RFH G Sbjct: 63 PKGQVVPEMSLAPVARHLSGILGMDVPLAPDCVGGAVRKMVDELEPGRVLLLENLRFHGG 122 Query: 123 ETKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFI-PSVAGFLMEKEIKFLSKV 181 ETKN+PE ++ A L D++VNDAF +HRAHAS GI +++ AG+ + KEI+ + Sbjct: 123 ETKNNPEFSRQLAELTDVYVNDAFAVSHRAHASVHGITEYVRECAAGYQLAKEIETFRQA 182 Query: 182 TYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEED 241 NP++P VV+GGAKVS KIGV+ NL+ K D ++IGGAM TFLKA GK VG+S VE++ Sbjct: 183 MENPQRPLAVVIGGAKVSTKIGVLENLIPKVDLLVIGGAMANTFLKAQGKSVGASLVEDE 242 Query: 242 KIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETI 301 ++ AK LL +A+E+GV ++LPVDA A ++ G + V +D +P D+G ET Sbjct: 243 FVETAKVLLAQARERGVRVILPVDATAAPSLDAGDRARQVPVDQ-VPPDLAIFDVGEETS 301 Query: 302 ELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAVN 361 L +Q L TVVWNGP+G FE F T +A +AA A TVVGGGDSAAAV Sbjct: 302 ALIRQALEPCATVVWNGPLGAFETPPFERATYDLARFLAA---SQAFTVVGGGDSAAAVA 358 Query: 362 KFGLEDKFSHVSTGGGASLEFLEGKELPGIASI 394 K G+ DK +VSTGGGA LE LEGK LPGI ++ Sbjct: 359 KAGVTDKVGYVSTGGGAFLEMLEGKVLPGIQAL 391 Lambda K H 0.317 0.137 0.386 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: 609 Number of extensions: 30 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: 654 Length of database: 398 Length adjustment: 34 Effective length of query: 620 Effective length of database: 364 Effective search space: 225680 Effective search space used: 225680 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: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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