Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate BPHYT_RS00720 BPHYT_RS00720 amidase
Query= SwissProt::Q38M35 (462 letters) >FitnessBrowser__BFirm:BPHYT_RS00720 Length = 475 Score = 162 bits (409), Expect = 3e-44 Identities = 144/476 (30%), Positives = 205/476 (43%), Gaps = 33/476 (6%) Query: 6 LSLAEHAARLRRRELTAVALIDTCAQHHARMEPRLNAYKTWDGARARSAAAAVDTLLDQG 65 LS A+ A R+ L+ V ++ +++P +NA+ D A SAA+ + +G Sbjct: 7 LSAAQLVAGFRQCTLSPVEVMCEVLDRITKLDPVVNAFCALDEEEAMSAASEAERRWMRG 66 Query: 66 QDLGPLMGLPVSVKDLYGVPGLPVFAGSDEALPEAWQAAGPLVARLQRQLGIVVGKTHTV 125 + GPL G+PVSVKDL V GLP GS A P+ P VARL+R I GKT T Sbjct: 67 EPCGPLDGVPVSVKDLVAVAGLPTRQGSWTASPDRESVDAPAVARLRRAGAIPFGKTTTS 126 Query: 126 EFAFGGLGVNAHWGTPRNPWSPHEHRVPGGSSAGAGVSLVQGSALLALGTDTAGSVRVPA 185 EF + G RNPW PGGSS G+ V++ G L+L TD GS+R+PA Sbjct: 127 EFGNKIVTDCPMTGATRNPWD--TRLSPGGSSGGSAVAVALGLGPLSLATDGGGSIRIPA 184 Query: 186 SMTGQVGLKTTVGRWPVEGIVPLSSSLDTAGVLTRTVEDLAYAFAALD-----TESQGLP 240 +G VG K T P G ++L T G +TRTV D A A+ S G P Sbjct: 185 CWSGVVGFKPTFALVPA-GSAASWTALSTLGPITRTVRDAALMLDAMTGTNTCANSDGPP 243 Query: 241 APAPVR---------VQGLRVGVPTNHFWDDIDPSIAAAVEAAVQRLAQAGAQVVRFPLP 291 V GLR+ + P IA V AV GA V+ + Sbjct: 244 GTGRTSAYSAGLDDGVAGLRIAWCAAPAGVSVAPDIAECVGRAVDAFGTLGATVIPTDV- 302 Query: 292 HCEEAFDIFRRGGLAASELAAYLDQHFPHKVER----LDPVVRDRVRWAEQVSSVEYLRR 347 D + G + + + + + Q H LDP + ++ + ++ Sbjct: 303 --APIVDYYGDGRIHSVQWSVFFAQRVRHMEAADRTLLDPDLTALADAGARIDTATFVDA 360 Query: 348 KAVLQRCGAGAARLFDDVDVLLTPTVPASPPRLADIGTVETYAPANMK-AMRNTAISNLF 406 GA F D+L+TPT PP + + P +++ A TA N Sbjct: 361 LLARHALGASMETFFKHYDLLVTPTFHCGPPPVPSL-------PGHLRNAPLLTAWCNQA 413 Query: 407 GWCALTMPVGLDANRMPVGLQLMGPPRAEARLIGIALGIEALIGQGHALLGAPDLP 462 G A+++P G A MP GLQ++G ++A ++ A E G A G LP Sbjct: 414 GVPAISVPCGF-AGDMPTGLQIIGRRGSDALVLRAARAYELARGDFPAPEGDLPLP 468 Lambda K H 0.320 0.135 0.411 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: 593 Number of extensions: 33 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: 462 Length of database: 475 Length adjustment: 33 Effective length of query: 429 Effective length of database: 442 Effective search space: 189618 Effective search space used: 189618 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: 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