Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_061535450.1 CAter10_RS18070 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_001584165.1:WP_061535450.1 Length = 394 Score = 310 bits (795), Expect = 6e-89 Identities = 174/377 (46%), Positives = 244/377 (64%), Gaps = 13/377 (3%) Query: 18 MRVDFNVPVKD-GVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRP-KGEPSPEFSLAP 75 +R D NVP D G + +DTRIRA++P I+ AL+ GA V++ SHLGRP +GE PE SLAP Sbjct: 20 IRADLNVPQDDAGNITEDTRIRASVPAIRQALDAGAAVMVTSHLGRPTEGEFKPEDSLAP 79 Query: 76 VAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGETKNDPELAKFWA 135 +AKRL+ELLG+ V+ V D V ++ G+V+LLEN R + GE KN ELA+ A Sbjct: 80 IAKRLAELLGQPVELKQNWV-DGV-----DVAPGQVVLLENCRVNKGEKKNSDELAQKIA 133 Query: 136 SLADIHVNDAFGTAHRAHASNVGIAQFIP-SVAGFLMEKEIKFLSKVTYNPEKPYVVVLG 194 L DI+VNDAFGTAHRA A+ GIA+F P + AG L+ E+ L K P +P V ++ Sbjct: 134 KLCDIYVNDAFGTAHRAEATTHGIAKFAPVACAGPLLAAELDALGKALNQPARPLVAIVA 193 Query: 195 GAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDKIDLAKELLEKAK 254 G+KVS K+ ++ L +K D +++GG + TFL A ++G S E D ++ AK ++E Sbjct: 194 GSKVSSKLTILKALADKVDNLIVGGGIANTFLLASRLKIGKSLAEPDLVEEAKAIIEMMA 253 Query: 255 EKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIELFKQKLSDAKTV 314 ++G + +PVD V A++ P ++ + D + E + LDIGP+T +++ A TV Sbjct: 254 KRGASVPIPVDVVCAKEFSPTAVAQIKDVGD-VAEDDLILDIGPKTAATLAAQIAQAGTV 312 Query: 315 VWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAVNKFGLEDKFSHVST 374 VWNGP+GVFE D F EGTK +ALAIA A ++ GGGD+ AA+ K+ + DK ++ST Sbjct: 313 VWNGPVGVFEFDQFGEGTKTLALAIA---NSKAFSIAGGGDTLAAIAKYNITDKIGYIST 369 Query: 375 GGGASLEFLEGKELPGI 391 GGGA LEFLEGK LP + Sbjct: 370 GGGAFLEFLEGKTLPAV 386 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: 592 Number of extensions: 30 Number of successful extensions: 6 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: 394 Length adjustment: 34 Effective length of query: 620 Effective length of database: 360 Effective search space: 223200 Effective search space used: 223200 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