Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate GFF3276 PGA1_c33270 amidase
Query= SwissProt::Q38M35 (462 letters) >FitnessBrowser__Phaeo:GFF3276 Length = 442 Score = 189 bits (479), Expect = 2e-52 Identities = 152/445 (34%), Positives = 205/445 (46%), Gaps = 17/445 (3%) Query: 8 LAEHAARLRRR----ELTAVALIDTCAQHHARMEPRLNAYKTWDGARARSAAAAVDTLLD 63 L + AA L R ++ VAL T R Y RA + A A Sbjct: 5 LTQTAANLGRGIDAGDICPVALTKTYLNAIDAHPHRDRIYTVVTHDRALAEAEAARQRAA 64 Query: 64 QGQDLGPLMGLPVSVKDLYGVPGLPVFAGSDEALPEAWQAAGPLVARLQRQLGIV-VGKT 122 GQ L L G+P+S KDL+ + +GSD L LV R +G V +GKT Sbjct: 65 DGQRLSLLDGVPISWKDLFDSATIATESGSD-LLANRIPDRDALVLRSATAMGAVCLGKT 123 Query: 123 HTVEFAFGGLGVNAHWGTPRNPWSPHEHRVPGGSSAGAGVSLVQGSALLALGTDTAGSVR 182 H E AF GLG+N TP P + PGGSS+GA S+ G A +G+DT GSVR Sbjct: 124 HMSELAFSGLGLNPVKATP--PCIHDDAAAPGGSSSGAATSVAFGLAACGIGSDTGGSVR 181 Query: 183 VPASMTGQVGLKTTVGRWPVEGIVPLSSSLDTAGVLTRTVEDLAYAFAALDTESQGLPAP 242 +PA+ G VGLKTT GR +EG+VPL DT G L R+VED A L E P Sbjct: 182 IPAAWNGLVGLKTTSGRISLEGVVPLCLRFDTVGPLARSVEDAALYLGVL--EGNHGPDL 239 Query: 243 APVRVQGLRVGVPTNHFWDDIDPSIAAAVEAAVQRLAQAGAQVVRFPLPHCEEAFDIFRR 302 + G R D+ P +A A A+ RL AGA+++ +P EEA + Sbjct: 240 RGASLAGKRFADLWTVAQQDLAPEVANAHSKALDRLRAAGAEIIPLEVPVLEEAMAL--S 297 Query: 303 GGLAASELAAYLDQHFPHKVERLDPVVRDRVRWAEQVSSVEYLRRKAVLQRCGAGAARLF 362 L SE + + P + +R R S +Y+ A L++ Sbjct: 298 AVLFTSEAYGLWKDVIEAAPDLMFPEILERFRSGAGFSGPDYVAAWAKLEQFRMDWDLAT 357 Query: 363 DDVDVLLTPTVPASPPRLADI-GTVETYAPANMKAMRNTAISNLFGWCALTMPVGLDANR 421 D +L PT P PP +A + + Y +N+ A+RNT I NL G CALT+P G+ + Sbjct: 358 AGFDGILCPTSPILPPNVARLQSDHDYYIHSNLMALRNTRIGNLMGLCALTLPTGVPS-- 415 Query: 422 MPVGLQLMGPPRAEARLIGIALGIE 446 GLQ++G P E L+ I +E Sbjct: 416 --CGLQILGQPDCEEALLRIGAAVE 438 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: 507 Number of extensions: 29 Number of successful extensions: 7 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: 442 Length adjustment: 33 Effective length of query: 429 Effective length of database: 409 Effective search space: 175461 Effective search space used: 175461 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