Align galactonate dehydratase (EC 4.2.1.6) (characterized)
to candidate RR42_RS34970 RR42_RS34970 bifunctional D-altronate/D-mannonate dehydratase
Query= BRENDA::G3Y8T6 (383 letters) >FitnessBrowser__Cup4G11:RR42_RS34970 Length = 403 Score = 172 bits (436), Expect = 1e-47 Identities = 124/398 (31%), Positives = 186/398 (46%), Gaps = 47/398 (11%) Query: 19 VKVTDSEDKFGWGEATLEGHTQAVEGAL-DEIIGRIVGYEADDIEHVWQTIWRLGFYRGG 77 +K+ E G G+ATL G AV L D + ++G + +E +WQ ++R ++R G Sbjct: 20 LKIETDEGLSGIGDATLNGRELAVASYLEDHVAPCLIGRDPHQVEDIWQYLYRGAYWRRG 79 Query: 78 PVFMSALSGIDIALWDLKGRRLNVPVYQLLGGKVRNKVQVYAWIGGDRPSDVEVAAKARI 137 PV MSA++ +D ALWD+K + +P+YQLLGGK R V VY G SD+E + Sbjct: 80 PVTMSAIAAVDTALWDIKAKAAGMPLYQLLGGKSRTGVMVYGHANG---SDIEATVDEVL 136 Query: 138 AQ---GLKCVKMNA-----------TEDMNWLDS-----PSVLDSCIERI---------K 169 G + V+ + + D + + PS D ER K Sbjct: 137 RYKELGYRAVRAQSGVPGLNKVYGVSSDRLFYEPADASLPSEHDWSTERYLDHTPRLFEK 196 Query: 170 QVKALGLDAGL--DFHGRLHRPMAKQLAKALEPYRPLFIEEPLLVEHPEAIKQLSQHTTI 227 A G D L D H RL A +L K+LEP+R ++E+ EH E+ + + QHTT Sbjct: 197 VRDAAGWDLHLLHDVHHRLTPIEAARLGKSLEPFRLFWMEDATPAEHQESFRLIRQHTTT 256 Query: 228 PIAFGERLYTRWDVKRFLEDASVDVLQPDIAHAGGISETKRIATMAETYDVAIAPH--CP 285 P+A GE T WD K +++ +D ++ + HAGGI+ +RIA A + V H Sbjct: 257 PLAVGEVFNTIWDCKTLIQEQLIDYIRATVVHAGGITHLRRIADFAAMHQVRTGSHGATD 316 Query: 286 LGPIALAASMQVALSTPNFVIQEMSLGMHYNVEAGDIDLTSYLTNPTVFNIEEGYVPAPT 345 L P+ + A++ L PNF IQE M ++ + + P + G + Sbjct: 317 LSPVCMGAALHFDLWVPNFGIQEY---MRHSEQTDAV-------FPHAYTFANGMLYPGD 366 Query: 346 GAGLGVEIDEELVRRISRETEPWLPKEFYGVDGGIREW 383 G GV+IDE L R + +LP DG + W Sbjct: 367 APGHGVDIDETLAARYPYQ-RAYLPVNRLAHDGTLWHW 403 Lambda K H 0.320 0.138 0.425 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: 412 Number of extensions: 28 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 383 Length of database: 403 Length adjustment: 31 Effective length of query: 352 Effective length of database: 372 Effective search space: 130944 Effective search space used: 130944 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 (21.8 bits) S2: 50 (23.9 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