Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate RR42_RS32650 RR42_RS32650 betaine-aldehyde dehydrogenase
Query= BRENDA::Q83XU8 (485 letters) >FitnessBrowser__Cup4G11:RR42_RS32650 Length = 484 Score = 736 bits (1899), Expect = 0.0 Identities = 351/462 (75%), Positives = 399/462 (86%) Query: 24 SPLNNAVIAKVHEAGRAEVDAAVAAAQAALKGAWGRMSLAQRVEVLYAVADGINRRFDDF 83 +P++N++IA+VHEAG+AEVDAAVAAA+ AL+G WG+M++A+RVE+L+AVADGINRRFDDF Sbjct: 23 NPVDNSLIARVHEAGQAEVDAAVAAAKQALRGPWGKMTVARRVEILHAVADGINRRFDDF 82 Query: 84 LAAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDGVGAINYAVRRP 143 L AE+ DTGKP SLA HVDIPRGAANFK+FAD++KNVPTE F M TPDG AINYAVR P Sbjct: 83 LQAEIADTGKPHSLASHVDIPRGAANFKVFADLIKNVPTESFAMATPDGGEAINYAVRSP 142 Query: 144 VGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPPGVY 203 GV+GV+CPWNLPLLLMTWKVGPALACGNTVVVKPSEETP TA LLGEVMN AGVPPGVY Sbjct: 143 RGVIGVVCPWNLPLLLMTWKVGPALACGNTVVVKPSEETPATATLLGEVMNEAGVPPGVY 202 Query: 204 NVVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADGARPVSLELGGKNAAIVF 263 NVVHGFGP+S G FLT+HPDVN ITFTGET TGEAIMKAAA+G RPVS ELGGKNA IVF Sbjct: 203 NVVHGFGPDSAGAFLTAHPDVNGITFTGETRTGEAIMKAAANGVRPVSFELGGKNAGIVF 262 Query: 264 ADCDLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEGMQLGRPEDLA 323 AD D DKA+ G RS F N GQVCLGTERVYV+RPIF RFV+ LK AE +++GRP D Sbjct: 263 ADADFDKAVAGITRSAFENSGQVCLGTERVYVQRPIFARFVAALKARAEALRIGRPNDEG 322 Query: 324 TGMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQPTIWTGLGDDS 383 MGPL+S EHR+KVLSYY+KA +AGATVVTGGGVPEMP AL GAWVQPTIWTGL +D+ Sbjct: 323 VNMGPLVSLEHRDKVLSYYRKAADAGATVVTGGGVPEMPGALAEGAWVQPTIWTGLPEDA 382 Query: 384 VVAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVGIAWV 443 V REEIFGPC + PFD+EEE IR AND YGLA +WT++L AHR+ A+EVGI W+ Sbjct: 383 AVIREEIFGPCCHIAPFDTEEEAIRLANDTPYGLAATVWTSDLGTAHRMGSALEVGICWI 442 Query: 444 NSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNVCIKL 485 N+WFLRDLRTAFGG+KQSGIGREGGVHSLEFYTEL+NVC+KL Sbjct: 443 NAWFLRDLRTAFGGAKQSGIGREGGVHSLEFYTELRNVCVKL 484 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: 728 Number of extensions: 17 Number of successful extensions: 1 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: 484 Length adjustment: 34 Effective length of query: 451 Effective length of database: 450 Effective search space: 202950 Effective search space used: 202950 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