Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate 206234 DVU0808 glutamyl-tRNA(Gln) amidotransferase, A subunit
Query= SwissProt::Q38M35 (462 letters) >MicrobesOnline__882:206234 Length = 489 Score = 178 bits (451), Expect = 4e-49 Identities = 160/482 (33%), Positives = 216/482 (44%), Gaps = 52/482 (10%) Query: 1 MNAAH-LSLAEHAARLRRRELTAVALIDTCAQHHARMEPRLNAYKTWDGARARSAAAAVD 59 M+A H LSLA L RRE+ A + C EPR++A A A A+D Sbjct: 1 MSALHTLSLAAIRDALARREVRAEDAVLDCLARIETTEPRIDALLHLRAEAAIEEARALD 60 Query: 60 TLLDQGQDLG-PLMGLPVSVKDLYGVPGLPVFAGSD--EALPEAWQAAGPLVARLQRQLG 116 G D PL G+PV+VKD G P AGS E + A V RL+ Sbjct: 61 AA---GPDASRPLWGVPVTVKDALTTAGTPTTAGSRILEDFVPFYDAFA--VQRLREAGA 115 Query: 117 IVVGKTHTVEFAFGGLGVNAHWGTPRNPWSPHEHRVPGGSSAGAGVSLVQGSALLALGTD 176 I++GK + EFA G N+ + RNPW RVPGGSS G+ S+ G +LGTD Sbjct: 116 IILGKNNMDEFAMGSSTENSAYKPTRNPWDTA--RVPGGSSGGSAASVAAGQCFASLGTD 173 Query: 177 TAGSVRVPASMTGQVGLKTTVGRWPVEGIVPLSSSLDTAGVLTRTVEDLAYAFAAL--DT 234 T GS+R PAS+ G VGLK T GR G++ SSLD G +TRTVED A + Sbjct: 174 TGGSIRQPASLCGCVGLKPTYGRVSRYGLIAYGSSLDQIGPMTRTVEDAAIVMGVIAGHD 233 Query: 235 ESQGLPAPAPVR-----------VQGLRVGVPTNHFWDDIDPSIAAAVEAAVQRLAQAGA 283 + A PV + G+R+GVP + + + P +A + AA+ GA Sbjct: 234 KRDSTCADRPVEDFAAALASRHDLAGVRIGVPAEFWGEGLSPEVATSCRAALDAARDLGA 293 Query: 284 QVVRFPLPHCEEAFDIFR--RGGLAASELAAY---------------LDQHFPHKVERLD 326 +V LPH ++ + A+S LA Y +D + + E L Sbjct: 294 TIVDVALPHTPQSIAAYYIVASAEASSNLARYDGVRYGKRAHAPEDLMDLYVRSRSEGLG 353 Query: 327 PVVRDRVRWAEQVSSVEY---LRRKA--VLQRCGAGAARLFDDVDVLLTPTVPASPPRLA 381 V+ R+ V S Y RKA V +R F DV+ P P + L Sbjct: 354 DEVQRRIMLGTYVLSSGYYDAYYRKAAQVRRRILEDYRNAFATCDVICGPVSPVTAWPLG 413 Query: 382 DIGTVETYAPANMKAMRNTAIS-NLFGWCALTMPVGLDA-NRMPVGLQLMGPPRAEARLI 439 + T P M M +S NL G L++PVGL + MPVG+QL+G EA L+ Sbjct: 414 AL----TADPLQMYLMDVFTLSLNLAGLPGLSLPVGLGTESGMPVGIQLLGRSFDEATLL 469 Query: 440 GI 441 + Sbjct: 470 SV 471 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: 548 Number of extensions: 33 Number of successful extensions: 5 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: 489 Length adjustment: 33 Effective length of query: 429 Effective length of database: 456 Effective search space: 195624 Effective search space used: 195624 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