Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate CCNA_03359 CCNA_03359 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >FitnessBrowser__Caulo:CCNA_03359 Length = 396 Score = 364 bits (935), Expect = e-105 Identities = 194/396 (48%), Positives = 261/396 (65%), Gaps = 12/396 (3%) Query: 5 TIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRPK 64 T+ DL GKR ++RVDFNVPV G V DDTR++AALPTI++ ++GAKV+LL+H RPK Sbjct: 5 TLDTADLAGKRALVRVDFNVPVDGGKVADDTRLKAALPTIRFLADKGAKVVLLAHFDRPK 64 Query: 65 GEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGET 124 G+ PE SLA VA+ L+ LLG V FV VG + V L +G V LLEN RFH GE Sbjct: 65 GKVVPEMSLAFVAEPLAALLGAPVAFVGDCVGPAAAEVVNGLADGGVALLENVRFHAGEE 124 Query: 125 KNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPSVAGFLMEKEIKFLSKVTYN 184 KND E AK A+ D++VNDAF AHRAHAS G+A+ +P+ G M++E++ L N Sbjct: 125 KNDAEFAKALAANGDVYVNDAFSAAHRAHASTEGLAKLLPAYPGVSMQRELEALDAALGN 184 Query: 185 PEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDKID 244 P+KP + ++GG+KVS K+ ++ NL+ K DR+ IGG M TFL A G +VG S E+D D Sbjct: 185 PKKPVIGIVGGSKVSTKLDLLNNLVAKLDRLAIGGGMANTFLFAQGHDVGGSLCEKDLAD 244 Query: 245 LAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKV-----VRIDDGIPEGWMGLDIGPE 299 A+E++EKAK G E++LPVD V+A+K+ PGVE V V+ DD I LD GPE Sbjct: 245 TAREIMEKAKAAGCELLLPVDVVVAKKVAPGVETAVRSLSEVQADDLI------LDAGPE 298 Query: 300 TIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAI-TVVGGGDSAA 358 + + + + T++WNGP+GVFE+ F E T A A+L + G I V GGGD+ A Sbjct: 299 SAKRLLAAMDQSLTLIWNGPLGVFEVPPFDEATVSAAKHAASLAKSGKIVAVAGGGDTVA 358 Query: 359 AVNKFGLEDKFSHVSTGGGASLEFLEGKELPGIASI 394 A+N G+ F+ VST GGA LE++EGK LPG+A++ Sbjct: 359 ALNHAGVSADFTFVSTAGGAFLEWMEGKTLPGVAAL 394 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: 627 Number of extensions: 35 Number of successful extensions: 3 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: 396 Length adjustment: 34 Effective length of query: 620 Effective length of database: 362 Effective search space: 224440 Effective search space used: 224440 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 17 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