Align 2-hydroxymuconic semialdehyde dehydrogenase; HMSD; EC 1.2.1.85 (characterized)
to candidate N515DRAFT_4232 N515DRAFT_4232 L-proline dehydrogenase /delta-1-pyrroline-5-carboxylate dehydrogenase
Query= SwissProt::P23105 (486 letters) >FitnessBrowser__Dyella79:N515DRAFT_4232 Length = 1074 Score = 160 bits (405), Expect = 2e-43 Identities = 143/471 (30%), Positives = 214/471 (45%), Gaps = 25/471 (5%) Query: 15 SASGKLFDNVSPANG-QVIGRVHEAGRAEVDAAVRAARAALKGPWGKMTVAERAEILHRV 73 +++G +PA+ QV+G A A V+ A+ A AA G W ++ A RA IL Sbjct: 590 TSAGATVQVTNPADRRQVVGSYVSADSATVEKALANAVAAQHG-WDRLPAASRAAILEHA 648 Query: 74 ADGITARFGEFLEARMPGHRQAEVAGQPHRHSARR--ANF-KVFADLLKNVANEAFEMAT 130 A+ + AR GEF+ + R+A G P + R A+F + +A + + + ++ Sbjct: 649 AEQLEARRGEFIALCV---REAG-KGLPDAIAEIREAADFLRYYATMARRYFGQPEQLPG 704 Query: 131 PDGAGALNYGVRRPKGVIGVISPWNLPLLLMTWKVGPALACGNCVVVKPSEETPLTATLL 190 P G N +GV ISPWN PL + +V ALA GN V+ KP+E+T L Sbjct: 705 PTGES--NQLFLNGRGVFVCISPWNFPLAIFLGQVAAALAAGNSVIAKPAEQTSLIGHAA 762 Query: 191 GEVMQAAGVPAGVYNVVHGFGGDSAGAFLTEHPDVDAYTFTGETGTGETIMRAAA---KG 247 +++ AGVPA V + G G + GA LT P V FTG T T I RA A Sbjct: 763 VQLLHEAGVPADVLQYLPG-DGATVGAALTRDPRVAGVAFTGSTETAWAINRALAARNAP 821 Query: 248 VRQVSLELGGKNAGIVFADCDMDKAIEGTLRSAFANCGQVCLGTERVYVERPIFDAFVAR 307 + + E GG+NA I + ++ ++ + SAF + GQ C +YV+ I D A Sbjct: 822 IAALIAETGGQNAMIADSSALPEQIVKDAVSSAFQSAGQRCSAARVLYVQEDIADKVCAM 881 Query: 308 LKAGAEALKIGEPNDPEANFGPLISHKPREKVPSYYQQAVDDGATVVTGGGVPEMPAHLA 367 L LK+G+P + GP+I R K+ + +D A + G V PA Sbjct: 882 LAGAMAELKVGDPAQLSTDVGPVIDEDAR-KILVDHAARMDQEAKKI--GEVALDPATTG 938 Query: 368 GGAWVQPTIWTGLADDSAVVTEEIFGPCCHIRPFDSEE--EAIELANSLPYGLASAIWTE 425 G + P + A +T EIFGP H+ + E + ++ N+ YGL I + Sbjct: 939 NGTFFAPRAYE--IPGLATLTREIFGPVLHVIRWKGSELDKVVDEINATGYGLTLGIHSR 996 Query: 426 NVRRAHRVAGQIEAGIVWVNSWFLRDL--RTAFGGSKQSGIG-REGGVHSL 473 + + G +VN + + FGG SG G + GG H L Sbjct: 997 IDDTVEFIQSRARVGNCYVNRNQIGAVVGVQPFGGEGLSGTGPKAGGPHYL 1047 Lambda K H 0.318 0.136 0.413 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: 1087 Number of extensions: 67 Number of successful extensions: 4 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: 486 Length of database: 1074 Length adjustment: 40 Effective length of query: 446 Effective length of database: 1034 Effective search space: 461164 Effective search space used: 461164 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 55 (25.8 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