Align 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate WP_011428504.1 RHE_RS27450 aldehyde dehydrogenase
Query= metacyc::MONOMER-13361 (500 letters) >NCBI__GCF_000092045.1:WP_011428504.1 Length = 504 Score = 333 bits (853), Expect = 1e-95 Identities = 186/479 (38%), Positives = 267/479 (55%), Gaps = 8/479 (1%) Query: 23 YIDGNFVT--SASSFANINPVNGKLISDVFEADAKQVNEAVVAAQNALKGP-WGKLSVQD 79 +I+G FV + + A+ +P G+ D+ ADA V AV AA A + P W +++ D Sbjct: 16 FINGEFVAPKAGNYIASYDPTTGERWYDLAAADANDVAAAVAAANAAFRNPAWRRMTQTD 75 Query: 80 RAALIHKIADGIQARFEEFVAAEVADTGRPVHQARTLDIPRAIANFRTFADLAKTSHTDL 139 R AL+ K+A+ ++A + E D G+ + + R + ++ FA +A D Sbjct: 76 RGALVRKLAELVRANADTLAEIETRDNGKLLKETRA-QMRSMPDSYHYFAGMADKLQGDT 134 Query: 140 FEMSTSDGSGALNYTVRKPLGVIGVISPWNLPLLLFTWKVAPALACGNTVVAKPSEESPS 199 ++ D LN +R+PLGV+G+I+PWN PL+L T +AP LA GNTVV KPSE + + Sbjct: 135 IPINRMD---TLNINLREPLGVVGMITPWNSPLMLLTGTLAPCLAIGNTVVIKPSEHATA 191 Query: 200 SATLLAEVMHDAGVPPGVFNLIHGFGKDSAGEFLTQHPGISALTFTGESKTGSTIMKAVA 259 S LAE++H+AG P GV N++ G GK SAGE LT+HPG++ FTG + TG I A Sbjct: 192 STLALAELIHEAGFPAGVVNVVTGTGK-SAGEALTRHPGVAKYVFTGSTATGRRIAGNAA 250 Query: 260 DGVKEVSFELGGKNAAVVFADADLDAAIEGVLRSSFTNSGQVCLCSERVYVHRSIFDEFV 319 + S ELGGK+ VVF D +L+ A+ GV+ F +GQ C+ R +V SI+D+F+ Sbjct: 251 QNLVPCSMELGGKSPHVVFGDVELEHAVNGVVSGVFAAAGQTCVAGSRCFVEASIYDKFI 310 Query: 320 SGLKVEAERLVVGYPDQDGVNMGPLISHGHRDKVLSYYRLAVDEGATVVTGGGVPKFNDE 379 L R+ VG P D ++GPL KV Y V +GA + GG P+ D Sbjct: 311 DALIARTARIRVGLPTLDDTDIGPLALADQLSKVEGYVASGVKDGAKIAAGGRRPRKEDL 370 Query: 380 RDQGAYVQPTIWTGLSDKARCVTEEIFGPVCHISPFDDEDEVINRVNDSNYGLACAIWTT 439 + G Y +PT+ + + +EIFGPV + PF DE E++ NDS+YGLA IWT Sbjct: 371 SNGGWYYEPTVMVDAQNDMGFMRDEIFGPVVGVMPFRDEAEMVALANDSHYGLASGIWTK 430 Query: 440 NLSRAHRVSRQIHVGLVWVNTWYLRDLRTPFGGVKLSGLGREGGRFSMDFYSDIANICI 498 ++ RA R + QI G VWVNT+ + GG K SG GR GG M +S + N+ I Sbjct: 431 DIDRALRFANQIEAGTVWVNTYRSASFMSANGGFKESGYGRRGGFEVMHEFSRLKNVII 489 Lambda K H 0.318 0.135 0.405 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: 585 Number of extensions: 23 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: 500 Length of database: 504 Length adjustment: 34 Effective length of query: 466 Effective length of database: 470 Effective search space: 219020 Effective search space used: 219020 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 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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