Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate CCNA_03242 CCNA_03242 succinic semialdehyde dehydrogenase
Query= BRENDA::Q83XU8 (485 letters) >FitnessBrowser__Caulo:CCNA_03242 Length = 485 Score = 277 bits (708), Expect = 7e-79 Identities = 164/459 (35%), Positives = 246/459 (53%), Gaps = 10/459 (2%) Query: 24 SPLNNAVIAKVHEAGRAEVDAAVAAAQAALKGAWGRMSLAQRVEVLYAVADGINRRFDDF 83 +P + +IA V + G AE A+ AA AL AW + +R +L +D I DD Sbjct: 31 NPADGTLIAAVADLGAAETTLAIDAAHRALP-AWAARTAKERGAILRRWSDLILAHADDL 89 Query: 84 LAAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDGVGAINYAVRRP 143 ++ GKP++ A+ ++ GA+ FA+ K P P G ++++P Sbjct: 90 ARLMTDEQGKPLAEAKG-EVVYGASFIDWFAEEAKRAYGHTIPTPMP---GKRLASIKQP 145 Query: 144 VGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPPGVY 203 VGV I PWN P+ ++T KVGPALA G TVVVKP+ ETP +A + + AGVP GV Sbjct: 146 VGVCAAIAPWNFPIAMITRKVGPALAAGCTVVVKPAAETPLSALAIARLATEAGVPAGVL 205 Query: 204 NVVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADGARPVSLELGGKNAAIVF 263 N+V + G+ L V ++FTG T G+ + + A + +SLELGG IVF Sbjct: 206 NIVTTTRSSEVGKVLCDDSRVRKLSFTGSTPIGKVLYQQCAGTMKKLSLELGGNAPFIVF 265 Query: 264 ADCDLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEGMQLGRPEDLA 323 D DL+ A++G + S + N GQ C+ R+ V+ I D F +RL + +++G Sbjct: 266 DDADLEAAVDGAIASKYRNAGQTCVCANRLIVQSGIHDAFAARLAEKVAALKVGPGTGEG 325 Query: 324 TGMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQPTIWTGLGDDS 383 +GPLI+++ KV+ AV+AGA V+TGG V + GG + QPT+ G + Sbjct: 326 VQIGPLINEKALTKVVGLVSGAVQAGAEVLTGGDVHGL-----GGHFYQPTVLVGATPEM 380 Query: 384 VVAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVGIAWV 443 + +EEIFGP A ++ F++E E + AN +GLA ++ ++ R RVA IE G+ + Sbjct: 381 RIFQEEIFGPVAPIVKFETEAEAVELANATPFGLAAYFYSRDVGRCWRVAEQIEAGMVGI 440 Query: 444 NSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNVC 482 N + FGG K+SG+GREG L+ Y E K +C Sbjct: 441 NEGLISTEVAPFGGVKESGLGREGASEGLDEYLETKYLC 479 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: 561 Number of extensions: 20 Number of successful extensions: 3 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