Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_013684376.1 ARCVE_RS08550 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_000194625.1:WP_013684376.1 Length = 406 Score = 206 bits (524), Expect = 2e-57 Identities = 143/416 (34%), Positives = 228/416 (54%), Gaps = 32/416 (7%) Query: 5 TIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRPK 64 T+ DV+ GK +++R+D N P+ + + D TR + +PT++ + K+++L+H RP Sbjct: 7 TLDDVEYDGKSILIRLDVNSPMVNSTILDTTRFESHVPTLEEL--ENTKLVVLAHQSRPG 64 Query: 65 GEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGET 124 + +L A+ LS LLG++V++V V ++ L+ GEVL+LEN RF+ E Sbjct: 65 KKDFT--TLESHAEVLSRLLGRDVEYVDECFSKRVIDRIKRLRRGEVLMLENVRFYAEER 122 Query: 125 --KNDPELAKFWA-----SLADIHVNDAFGTAHRAHASNVGIAQFIPSVAGFLMEKEIKF 177 ++ E A + S D+ VNDAF T HR HAS +G +PSV G L+EKE+ Sbjct: 123 LDRSAEEHASSFIVRRLYSNFDLFVNDAFSTCHRGHASLIGFPPVLPSVVGRLVEKEVTA 182 Query: 178 LSKVTYNPEKPYVVVLGGAKVSDKIGVITNLMEK--ADRILIGGAMMFTFLKALGKEVGS 235 LSK E V +LGGAK+ D + V+ N++ A+++++ G + FL GK++G Sbjct: 183 LSK-ALKGEGRKVFILGGAKIDDSVKVMKNVLTNGIAEKVILTGVVANYFLMLDGKDIGE 241 Query: 236 S--RVEED---KIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEG 290 + ++ ED K+D E+LE ++ IVLPVD +E +K V ID+ +G Sbjct: 242 ANRKIVEDSKEKVD-DGEMLELLRKYRDRIVLPVDVA----VEVDGRRKDVGIDE--VDG 294 Query: 291 WMGLDIGPETIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITV 350 +DIG TI + ++ V NGP GVFE + F GT +V A++ + +V Sbjct: 295 RKIMDIGVNTISMLMDEIPSYDVAVINGPAGVFEDERFTLGTFEVLKAVS----RAGFSV 350 Query: 351 VGGGDSAAAVNKFGLEDKFSHVSTGGGASLEFLEGKELPGIASIAD--KKKITRKL 404 VGGG + A G++ + HVST GGA + FL G++L + I + +KK + K+ Sbjct: 351 VGGGHISTAARMIGIDKRMDHVSTAGGACIRFLSGEKLIALEVIKEYWEKKWSAKV 406 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: 620 Number of extensions: 31 Number of successful extensions: 7 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: 406 Length adjustment: 35 Effective length of query: 619 Effective length of database: 371 Effective search space: 229649 Effective search space used: 229649 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 Apr 10 2024. The underlying query database was built on Apr 09 2024.
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