Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate AZOBR_RS19635 AZOBR_RS19635 succinate-semialdehyde dehydrogenase
Query= BRENDA::Q83XU8 (485 letters) >FitnessBrowser__azobra:AZOBR_RS19635 Length = 485 Score = 295 bits (756), Expect = 2e-84 Identities = 175/463 (37%), Positives = 263/463 (56%), Gaps = 10/463 (2%) Query: 23 SSPLNNAVIAKVHEAGRAEVDAAVAAAQAALKGAWGRMSLAQRVEVLYAVADGINRRFDD 82 ++P +A+V + G E A+ AA AAL AW + +R +L + I +D Sbjct: 31 TNPATGEELAQVADVGAEETRQAINAADAALP-AWRAKTAKERAAILRRWFELIMAAQED 89 Query: 83 FLAAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDGVGAINYAVRR 142 + GKP++ AR ++ GA+ + FA+ K V + +P+ G I ++ Sbjct: 90 LAVLMTLEQGKPLAEARG-EVAYGASFIEWFAEEGKRVYGDV--IPSFAGNKRI-VVLKE 145 Query: 143 PVGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPPGV 202 P+GVV I PWN P ++T KVGPALA G T+VVKP+E+TP +A L E+ AGVP GV Sbjct: 146 PIGVVAAITPWNFPNAMITRKVGPALAAGCTIVVKPAEDTPLSALALAELAERAGVPAGV 205 Query: 203 YNVVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADGARPVSLELGGKNAAIV 262 +N+V G P + G LT+ P V ++FTG T G+ +M+ +AD + VSLELGG IV Sbjct: 206 FNIVTGSDPVAIGGELTASPIVRKLSFTGSTEVGKILMRQSADTVKKVSLELGGNAPFIV 265 Query: 263 FADCDLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEGMQLGRPEDL 322 F D DLD+A++G L S + N GQ C+ R+ V+ ++D F ++L + + +++G + Sbjct: 266 FDDADLDEAVKGALASKYRNSGQTCVCANRLLVQAGVYDAFAAKLAEAVKQIRVGNGMEA 325 Query: 323 ATGMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQPTIWTGLGDD 382 GP+I+ + EKV A+ GA V GG + GG + +PTI TG+ + Sbjct: 326 GVTQGPMINGQAVEKVEELMGDALAKGAKVALGGKRHGL-----GGTFFEPTILTGVTTE 380 Query: 383 SVVAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVGIAW 442 VAREEIFGP A + F++E + IR AND ++GLA ++ ++ R RVA +E G+ Sbjct: 381 MRVAREEIFGPVAPLFKFETEADAIRMANDTEFGLAAYFYSRDIGRVWRVAEQLEYGMVG 440 Query: 443 VNSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNVCIKL 485 +N L FGG KQSGIGREG + +E + E+K +C+ L Sbjct: 441 INEGILSTEVAPFGGIKQSGIGREGSKYGVEDFLEIKYLCVGL 483 Lambda K H 0.318 0.135 0.406 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: 539 Number of extensions: 26 Number of successful extensions: 2 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: 485 Length of database: 485 Length adjustment: 34 Effective length of query: 451 Effective length of database: 451 Effective search space: 203401 Effective search space used: 203401 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: 52 (24.6 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