Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_058858667.1 AS188_RS09630 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_001482365.1:WP_058858667.1 Length = 407 Score = 354 bits (908), Expect = e-102 Identities = 190/394 (48%), Positives = 260/394 (65%), Gaps = 15/394 (3%) Query: 13 GKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRPKGEPSPEFS 72 G+RV++R D NVP+ V DD R+RA+LP I+ GA+VI+++HLGRPKG+ P++S Sbjct: 15 GRRVLVRSDLNVPLDGVTVTDDGRVRASLPVIEKLAHAGARVIVMAHLGRPKGQVDPKYS 74 Query: 73 LAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGET-KNDPELA 131 +AP +RL+EL V+ VVG + + L +GEVL+LEN RF P ET K+D E Sbjct: 75 IAPAGQRLAELADVPVRIATDVVGQDARDKAAALADGEVLVLENVRFDPRETSKDDAERG 134 Query: 132 KFWASLADI------HVNDAFGTAHRAHASNVGIAQFIPSVAGFLMEKEIKFLSKVTYNP 185 LA + +V DAFG HR HAS IA +P+ G L+ +E++ L+KV +P Sbjct: 135 ALADELAALTGENGAYVGDAFGAVHRKHASVYDIAHRLPAYQGDLVRRELEVLTKVVQDP 194 Query: 186 EKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDKIDL 245 E+P+VVV+GG+KVSDK+ VI NL+ +AD +LIGG M+FTFL A G VG S +EED+++ Sbjct: 195 ERPFVVVMGGSKVSDKLAVIDNLIGRADALLIGGGMVFTFLAAQGHRVGGSLLEEDQLET 254 Query: 246 AKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDD----GIPEGWMGLDIGPETI 301 K LE+A + G EIVLPVD V A++ + ++D I +GLDIGP + Sbjct: 255 VKGYLERAADAGTEIVLPVDVVYAERFAADAPHETRPVEDIVGGQIGASGLGLDIGPASA 314 Query: 302 ELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAAAVN 361 LF ++ A+TV WNGPMGVFE+D FA GT+ VA AI A A++V+GGGDSA+AV Sbjct: 315 ALFADRIKAARTVFWNGPMGVFEMDAFAAGTRAVAEAIVA---SEAMSVIGGGDSASAVR 371 Query: 362 KFGLED-KFSHVSTGGGASLEFLEGKELPGIASI 394 G D +F H+STGGGASLEF+EGKELPG+ ++ Sbjct: 372 NLGFTDEQFGHISTGGGASLEFIEGKELPGVVAL 405 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: 681 Number of extensions: 29 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: 407 Length adjustment: 35 Effective length of query: 619 Effective length of database: 372 Effective search space: 230268 Effective search space used: 230268 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