Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate 6936634 Sama_0822 fumarate hydratase (RefSeq)
Query= BRENDA::Q9HTD7 (474 letters) >FitnessBrowser__SB2B:6936634 Length = 457 Score = 316 bits (810), Expect = 9e-91 Identities = 196/461 (42%), Positives = 264/461 (57%), Gaps = 19/461 (4%) Query: 7 SRIEKDLLGTLEVPADAYYGIQTLRAVNNFRLSGVPLSHYPKLVVALAMVKQAAADANRQ 66 SRIE D +G + VPA+A YG QT RA+NNF + G P+ + L ++K AAA AN Q Sbjct: 3 SRIETDSMGEVLVPAEALYGAQTQRALNNFAIGGQPMPR--AFIETLLLIKAAAARANSQ 60 Query: 67 LGHLPEDKHAAISEACARLIRGD-FHEQFVVDMIQGGAGTSTNMNANEVIANIALEAMGH 125 LG L D AI+EA L + + F VD+ Q G+GTS+NMNANEV+A + E++G Sbjct: 61 LGVLASDCGQAITEAALSLRQDKALMQHFPVDVFQTGSGTSSNMNANEVLARLTSESLGR 120 Query: 126 TKGEYKYLHPNNDVNMAQSTNDAYPTAIRL---GLLLGHDTLLASLDSLIQAFAAKGVEF 182 + N++VN+ QS+ND P+ I++ G+L TLL +L L K Sbjct: 121 A------VSANDEVNLGQSSNDVIPSCIQIASAGVLT--KTLLPALTHLKSCIRTKAASV 172 Query: 183 AGVLKMGRTQLQDAVPMTLGQEFHAFATTLGEDLDRLRRLAPELLT--EVNLGGTAIGTG 240 GV+K GRT L DA+P+ L Q +A+ L R +L +L++ ++ GGTA+GTG Sbjct: 173 KGVVKTGRTHLMDAMPVRLSQSLETWASQLDA---RELQLQSQLISLWQLPQGGTAVGTG 229 Query: 241 INADPGYQKLAVERLAAISGQPLKPAADLIEATSDMGAFVLFSGMLKRTAVKLSKICNDL 300 +NA PG+ + L ++G +PA L + V SG LK AV L KI NDL Sbjct: 230 VNAAPGFPQAFCHELNLLTGLAFQPAPHLFTGIASQDTAVALSGELKALAVTLMKIANDL 289 Query: 301 RLLSSGPRTGINEINLPPRQPGSSIMPGKVNPVIPEAVNQVAFEVIGNDLALTLAAEGGQ 360 R ++SGP G+ EI LP QPGSSIMPGKVNPVIPEAV +VIGND +T+A + G Sbjct: 290 RWMNSGPLAGLGEIRLPALQPGSSIMPGKVNPVIPEAVAMACAQVIGNDACITVAGQSGN 349 Query: 361 LQLNVMEPLIAYKIFDSIRLLQRAMDMLREHCITGITANVERCHELVEHSIGLVTALNPY 420 +LNVM P+IA + S+RLL AM L + I G R + + + LVTALNP Sbjct: 350 FELNVMLPVIADNLLSSLRLLTNAMMALADKAIDGFEVCEGRMAKELSRNPILVTALNPI 409 Query: 421 IGYENSTRIAKTALESGRGVLELVREEKLLDEATLADILLP 461 +GY + IAK A GR VLE+ E +D LA +L P Sbjct: 410 VGYAKAADIAKRAYAEGRPVLEVALEMTDIDAEELARLLDP 450 Lambda K H 0.318 0.135 0.380 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: 519 Number of extensions: 22 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: 474 Length of database: 457 Length adjustment: 33 Effective length of query: 441 Effective length of database: 424 Effective search space: 186984 Effective search space used: 186984 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 (21.7 bits) S2: 51 (24.3 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