Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate RR42_RS32650 RR42_RS32650 betaine-aldehyde dehydrogenase
Query= BRENDA::Q1XGK8 (486 letters) >FitnessBrowser__Cup4G11:RR42_RS32650 Length = 484 Score = 743 bits (1917), Expect = 0.0 Identities = 361/486 (74%), Positives = 405/486 (83%), Gaps = 2/486 (0%) Query: 1 MKEIKHFINGAFVGSASGRTFEDINPSNGQVIGHVHEAGRAEVDAAVKAARAALKGPWGK 60 MKE K+FING +V A+ R F+D NP + +I VHEAG+AEVDAAV AA+ AL+GPWGK Sbjct: 1 MKEFKNFINGEWV--ATNRRFDDRNPVDNSLIARVHEAGQAEVDAAVAAAKQALRGPWGK 58 Query: 61 LSVAERAEILHRVADGITARFDEFLEAECLDTGKPKSLASHIDIPRGAANFKVFADLLKN 120 ++VA R EILH VADGI RFD+FL+AE DTGKP SLASH+DIPRGAANFKVFADL+KN Sbjct: 59 MTVARRVEILHAVADGINRRFDDFLQAEIADTGKPHSLASHVDIPRGAANFKVFADLIKN 118 Query: 121 VANEAFEMATPDGAGAINYAVRRPKGVIGVISPWNLPLLLMTWKVGPALACGNTVVVKPS 180 V E+F MATPDG AINYAVR P+GVIGV+ PWNLPLLLMTWKVGPALACGNTVVVKPS Sbjct: 119 VPTESFAMATPDGGEAINYAVRSPRGVIGVVCPWNLPLLLMTWKVGPALACGNTVVVKPS 178 Query: 181 EETPLTATLLGEVMQAAGVPAGVYNVVHGFGGDSAGAFLTEHPDVDAYTFTGETGTGEVI 240 EETP TATLLGEVM AGVP GVYNVVHGFG DSAGAFLT HPDV+ TFTGET TGE I Sbjct: 179 EETPATATLLGEVMNEAGVPPGVYNVVHGFGPDSAGAFLTAHPDVNGITFTGETRTGEAI 238 Query: 241 MRAAAKGVRQVSLELGGKNAGIVFADCDMDKAIEGTLRSAFANCGQVCLGTERVYVERPI 300 M+AAA GVR VS ELGGKNAGIVFAD D DKA+ G RSAF N GQVCLGTERVYV+RPI Sbjct: 239 MKAAANGVRPVSFELGGKNAGIVFADADFDKAVAGITRSAFENSGQVCLGTERVYVQRPI 298 Query: 301 FDEFVARLKAGAESLMIGPPDDASSNFGPLVSLKHREKVLSYYQQAVDDGGSVITGGGVP 360 F FVA LKA AE+L IG P+D N GPLVSL+HR+KVLSYY++A D G +V+TGGGVP Sbjct: 299 FARFVAALKARAEALRIGRPNDEGVNMGPLVSLEHRDKVLSYYRKAADAGATVVTGGGVP 358 Query: 361 DMPAHLAGGAWVQPTIWTGLSDDSAVVTEEIFGPCCHIRPFDTEEEAIELANSLPYGLAS 420 +MP LA GAWVQPTIWTGL +D+AV+ EEIFGPCCHI PFDTEEEAI LAN PYGLA+ Sbjct: 359 EMPGALAEGAWVQPTIWTGLPEDAAVIREEIFGPCCHIAPFDTEEEAIRLANDTPYGLAA 418 Query: 421 AIWTENGSRAHRVAGQIEAGIVWVNSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELK 480 +WT + AHR+ +E GI W+N+WFLRDLRTAFGG+KQSGIGREGGVHSLEFYTEL+ Sbjct: 419 TVWTSDLGTAHRMGSALEVGICWINAWFLRDLRTAFGGAKQSGIGREGGVHSLEFYTELR 478 Query: 481 NICVKL 486 N+CVKL Sbjct: 479 NVCVKL 484 Lambda K H 0.318 0.136 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: 830 Number of extensions: 33 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: 486 Length of database: 484 Length adjustment: 34 Effective length of query: 452 Effective length of database: 450 Effective search space: 203400 Effective search space used: 203400 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