Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_024850290.1 N745_RS0101040 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_000526715.1:WP_024850290.1 Length = 392 Score = 335 bits (858), Expect = 3e-96 Identities = 186/401 (46%), Positives = 257/401 (64%), Gaps = 11/401 (2%) Query: 1 MEKMTIRDVDLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHL 60 M + + D+DL GKRV++R D NVPVK+G V D RIRA+LPTIK A + GAKV+L+SHL Sbjct: 1 MSVIKMSDLDLAGKRVLIREDLNVPVKEGKVTSDARIRASLPTIKMAADAGAKVMLMSHL 60 Query: 61 GRP-KGEPSPEFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRF 119 GRP +GE + EFSLAPVA LS LGKEV+ V + ++ +GEV+LLEN RF Sbjct: 61 GRPSEGEYAEEFSLAPVAADLSAKLGKEVRLVKDYLDGGF-----DVADGEVVLLENVRF 115 Query: 120 HPGETKNDPELAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPSV-AGFLMEKEIKFL 178 + GE KND L+K +A+L D++V DAFGTAHRA AS G F + AG L+ E+ L Sbjct: 116 NVGEKKNDEALSKKYAALCDVYVMDAFGTAHRAQASTHGAGAFADTACAGPLLAAELDAL 175 Query: 179 SKVTYNPEKPYVVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRV 238 K NP +P V ++GG+KVS K+ V+ +L EK D++++GG + TF++A G VG S Sbjct: 176 GKALNNPARPMVAIVGGSKVSTKLTVLESLSEKVDQLVVGGGIANTFIEAAGYNVGKSLS 235 Query: 239 EEDKIDLAKELLEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGP 298 E D I K+L E + +G I L D V ++ + + D + + M DIGP Sbjct: 236 ETDLIPTCKKLNEIMESRGAAIPLASDVVCGKEFSESAAAETKNVAD-VADDDMIFDIGP 294 Query: 299 ETIELFKQKLSDAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAITVVGGGDSAA 358 ++ + +A TVVWNGP+GVFE D F EGTK +++AIA E A ++ GGGD+ A Sbjct: 295 DSAAELATIIKNAGTVVWNGPVGVFEFDQFGEGTKAISMAIA---ESSAFSIAGGGDTLA 351 Query: 359 AVNKFGLEDKFSHVSTGGGASLEFLEGKELPGIASIADKKK 399 A++K+ + DK S++STGGGA LEFLEGK+LP + + + K Sbjct: 352 AIDKYDIADKVSYISTGGGAFLEFLEGKKLPAVEMLENAAK 392 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: 591 Number of extensions: 38 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: 392 Length adjustment: 34 Effective length of query: 620 Effective length of database: 358 Effective search space: 221960 Effective search space used: 221960 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 Apr 09 2024. 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