Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_043769244.1 U743_RS14650 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_000733765.1:WP_043769244.1 Length = 392 Score = 330 bits (846), Expect = 7e-95 Identities = 184/399 (46%), Positives = 262/399 (65%), Gaps = 12/399 (3%) Query: 1 MEKMTIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHL 60 M + + D+DL GKR+++R D NVP+ G + D R+RAALPT+K ALE GA V++LSHL Sbjct: 1 MAILRMSDLDLAGKRLLIRQDLNVPISGGYITSDARLRAALPTLKQALEAGASVLVLSHL 60 Query: 61 GRPK-GEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRF 119 GRPK G P+ SL VA LSE L + V +V D ++ EL G++ L ENTRF Sbjct: 61 GRPKPGHLDPDNSLTLVAAWLSEQLDRVVP----LVSDWIEGV--ELAPGQIALGENTRF 114 Query: 120 HPGETKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIP-SVAGFLMEKEIKFL 178 GE +ND L++ A L DI+VNDAFGTAHRA AS G+A+F + AG L+ E++ L Sbjct: 115 AAGEKENDETLSRKMAELCDIYVNDAFGTAHRAEASTHGVARFAKVACAGPLLSAELEAL 174 Query: 179 SKVTYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRV 238 K NP++P VV++GGAKVS K+ ++TNL +KAD++++GG + TFL A G +VG S Sbjct: 175 GKAVANPKRPQVVIVGGAKVSTKLDLLTNLADKADQLIVGGGIANTFLAAAGFKVGKSLH 234 Query: 239 EEDKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGP 298 E D +D A+ + E+ + G +I LP D V+A +I +V ++ D + + M LDIGP Sbjct: 235 EPDMLDTARAIHERIRANGGDIPLPEDVVVATEISSEARAEVRQVGD-VLDDEMILDIGP 293 Query: 299 ETIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAA 358 ++ L +A ++VWNGP+GVFE D FA GT+ +A AIA + A ++ GGGD+ A Sbjct: 294 KSARALGASLRNAGSIVWNGPVGVFEYDAFAAGTRILAHAIA---DSDAFSLAGGGDTLA 350 Query: 359 AVNKFGLEDKFSHVSTGGGASLEFLEGKELPGIASIADK 397 A++ FG+ D+ S++STGGGA LEFLEGK LP + + ++ Sbjct: 351 AIDTFGVADRISYISTGGGAFLEFLEGKTLPAVGILEER 389 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: 590 Number of extensions: 37 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: 392 Length adjustment: 34 Effective length of query: 620 Effective length of database: 358 Effective search space: 221960 Effective search space used: 221960 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