Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_079557420.1 CDL62_RS10145 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_002201795.1:WP_079557420.1 Length = 419 Score = 378 bits (971), Expect = e-109 Identities = 199/416 (47%), Positives = 277/416 (66%), Gaps = 29/416 (6%) Query: 6 IRDVDLKGKRVIMRVDFNVPVKDGV-VQDDTRIRAALPTIKYALEQGAKVILLSHLGRPK 64 I + + GK+ I+RVDFNVP + + DDTRIRAA+PTI+ L+ G I++SHLGRPK Sbjct: 4 IENYNFSGKKAIVRVDFNVPFNEKFEITDDTRIRAAMPTIQKILKDGGSAIIMSHLGRPK 63 Query: 65 GEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGET 124 G+ +P+FSL + L++ +G +V F VG EVK E LK G++LLLEN RF+ E Sbjct: 64 GKVNPDFSLNHIKAHLAKTVGTDVIFAGDCVGSEVKAKAESLKPGQILLLENLRFYL-EE 122 Query: 125 KNDPEL-----------------------AKFWASLADIHVNDAFGTAHRAHASNVGIAQ 161 + P+L +K ASLAD++VNDAFGTAHRAHAS IA Sbjct: 123 EGKPKLPEGASDEETKVAKAEMKEKQKAFSKELASLADVYVNDAFGTAHRAHASTAVIAD 182 Query: 162 FIPS---VAGFLMEKEIKFLSKVTYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIG 218 + + + GFL+E E++ L KV P++P+ ++GGAKVS KI +I NL++K D +++G Sbjct: 183 YFDTDSKMFGFLIESEVQSLDKVVKEPKRPFTAIMGGAKVSSKITIIENLLDKVDNLILG 242 Query: 219 GAMMFTFLKALGKEVGSSRVEEDKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEK 278 G M FTF+KA G +VG+S E++ +DLAKE+ +KAKEKGV ++L D V Sbjct: 243 GGMTFTFMKARGGKVGNSICEDEYLDLAKEIEKKAKEKGVNLLLASDVVAGDSFSNDANT 302 Query: 279 KVVRIDDGIPEGWMGLDIGPETIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALA 338 ++V DD IPEGW GLD GP +++ F + ++ T++WNGP+GVFE+D FA+G++ VA A Sbjct: 303 QIVSADD-IPEGWEGLDAGPNSVKEFCHVIENSATILWNGPVGVFEMDTFAKGSRAVADA 361 Query: 339 IAALTEKGAITVVGGGDSAAAVNKFGLEDKFSHVSTGGGASLEFLEGKELPGIASI 394 I A T+KGA +++GGGDS A +NKFGL D S++ST GGA LE+LEGKELPGI +I Sbjct: 362 IVAGTKKGAFSLIGGGDSVACINKFGLADGVSYISTAGGALLEYLEGKELPGIKAI 417 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: 679 Number of extensions: 38 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: 419 Length adjustment: 35 Effective length of query: 619 Effective length of database: 384 Effective search space: 237696 Effective search space used: 237696 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