Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate PfGW456L13_3652 Aspartyl-tRNA(Asn) amidotransferase subunit A (EC 6.3.5.6) @ Glutamyl-tRNA(Gln) amidotransferase subunit A (EC 6.3.5.7)
Query= SwissProt::Q38M35 (462 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3652 Length = 482 Score = 168 bits (426), Expect = 3e-46 Identities = 139/471 (29%), Positives = 221/471 (46%), Gaps = 33/471 (7%) Query: 4 AHLSLAEHAARLRRRELTAVALIDTCAQHHARMEPRLNAYKTWDGARARSAAAAVDTLLD 63 + L +A AA +RR ++++ + + A L A+ T D A +AA A DT Sbjct: 15 SELGVAAAAAAIRRGDISSESYTAALLRR-AHTFSDLGAFITIDEAAVLAAARACDTARA 73 Query: 64 QGQDLGPLMGLPVSVKDLYGVPGLPVFAGSDEALPEAWQAAGPLVARLQRQLGIVVGKTH 123 G PL+G+PV+VKD Y GL G +V ++ GIV GK + Sbjct: 74 TGST-APLLGVPVAVKDSYLTQGLRTTLGIRSLENFVPARDAEVVRAIKDAGGIVFGKNN 132 Query: 124 TVEFAFGGLGVNAHWGTPRNPWSPHEHRVPGGSSAGAGVSLVQGSALLALGTDTAGSVRV 183 VE ++G G N+H+G +NP +P EH V GGSS+GAG S+ ALG DT GS+RV Sbjct: 133 LVEMSYGLTGHNSHFGQAKNPHNP-EH-VTGGSSSGAGASVGAQIVPAALGGDTVGSIRV 190 Query: 184 PASMTGQVGLKTTVGRWPVEGIVPLSSSLDTAGVLTRTVEDLAYAFAALDTESQGLPAPA 243 PAS G VG K + GRW +GI P+S +LDTAGV RTVED A + T++ Sbjct: 191 PASFCGVVGFKPSPGRWSGDGIAPISHTLDTAGVFARTVEDCALIDQVV-TKTTSTVHGD 249 Query: 244 PVRVQGLRVGVPTNHFWDDIDPSIAAAVEAAVQRLAQAGAQVVRFPLPHCEEAFDIFRRG 303 ++G+R+ + I+ + + ++RL AGA+VV L E+ F + R Sbjct: 250 WTGLRGIRLAYAPRQHLERINHEVEEHFKETIRRLCDAGAEVVEVDLG--EDFFAMTERS 307 Query: 304 GLA------ASELAAYLDQH-----FPHKVERLDPVVRDRVRWAEQV-----SSVEYLRR 347 + +A +L ++ F L P ++D W V + + Sbjct: 308 TWSIFFHETMESVAGFLRKNRIPSSFEDIYNELKPGLKD--AWGHLVLPSGAGFISHETY 365 Query: 348 KAVLQRCGAGAARLFD------DVDVLLTPTVPASPPRLADIG--TVETYAPANMKAMRN 399 + L R F+ L+ PT P P + T+ ++ R+ Sbjct: 366 QTALDHDRPEIQRRFNMAFSSSGAQALIMPTTPCPAPTIEQQTKFTIAGQEVDDLALARH 425 Query: 400 TAISNLFGWCALTMPVGLDANRMPVGLQLMGPPRAEARLIGIALGIEALIG 450 T ++ G +++P+G+ +N +P+GL++ G + +L+ +A +EA +G Sbjct: 426 TVAGSIAGLPGISIPMGMSSNGLPIGLEIDGKNGDDRKLLELARRVEAAVG 476 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: 525 Number of extensions: 25 Number of successful extensions: 5 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: 462 Length of database: 482 Length adjustment: 33 Effective length of query: 429 Effective length of database: 449 Effective search space: 192621 Effective search space used: 192621 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