Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate PP_4963 PP_4963 Phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >FitnessBrowser__Putida:PP_4963 Length = 387 Score = 327 bits (838), Expect = 6e-94 Identities = 186/401 (46%), Positives = 254/401 (63%), Gaps = 17/401 (4%) Query: 1 MEKMTIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHL 60 M + + D+DL+GKRV++R D NVPVKDGVV D RI AALPTIK ALE+GA V++ SHL Sbjct: 1 MTVLKMTDLDLQGKRVLIREDLNVPVKDGVVASDARILAALPTIKLALEKGAAVMVCSHL 60 Query: 61 GRP-KGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRF 119 GRP +GE S E SL PVA LS+ LG++V V + +A GE++L EN RF Sbjct: 61 GRPTEGEFSAENSLKPVADYLSKALGRDVPLVADYLDGVAVQA------GELVLFENVRF 114 Query: 120 HPGETKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIP-SVAGFLMEKEIKFL 178 + GE KN ELA+ +A+L D+ V DAFGTAHRA S G+A+F + AG L+ E+ L Sbjct: 115 NKGEKKNADELAQKYAALCDVFVMDAFGTAHRAEGSTHGVAKFAKVAAAGPLLAAELDAL 174 Query: 179 SKVTYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRV 238 K P KP ++ G+KVS K+ V+ +L D++++GG + TFL A G VG S Sbjct: 175 GKALKAPAKPMAAIVAGSKVSTKLDVLNSLSSVCDQLIVGGGIANTFLAAAGHPVGKSLY 234 Query: 239 EEDKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGP 298 E D +D AK + K V + LPVD V+A++ E V I D + M LDIGP Sbjct: 235 EPDLVDTAKAIAAK-----VSVPLPVDVVVAKEFAESAEATVKAIAD-VAADDMILDIGP 288 Query: 299 ETIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAA 358 +T F + L +KT++WNGP+GVFE D F GTK +A AIA + A ++ GGGD+ A Sbjct: 289 QTAANFAELLKSSKTILWNGPVGVFEFDQFGNGTKVLAKAIA---DSAAFSIAGGGDTLA 345 Query: 359 AVNKFGLEDKFSHVSTGGGASLEFLEGKELPGIASIADKKK 399 A++K+G+ + S++STGGGA LEF+EGK LP +A + ++ K Sbjct: 346 AIDKYGVSKEISYISTGGGAFLEFVEGKVLPAVAILEERAK 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: 564 Number of extensions: 28 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: 387 Length adjustment: 34 Effective length of query: 620 Effective length of database: 353 Effective search space: 218860 Effective search space used: 218860 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