Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_104913707.1 C3B54_RS06115 gamma-aminobutyraldehyde dehydrogenase
Query= metacyc::MONOMER-15108 (486 letters) >NCBI__GCF_002950575.1:WP_104913707.1 Length = 478 Score = 294 bits (752), Expect = 5e-84 Identities = 175/475 (36%), Positives = 261/475 (54%), Gaps = 15/475 (3%) Query: 13 HFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANE 72 +FI+G++V S +T ++PATEE AA++D A QAA KA G W + T E Sbjct: 8 NFINGQYVDSKGSETIPLVDPATEEVYAHSPISSAADVDDAYQAASKAFEG-WSETTPAE 66 Query: 73 RIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEA 132 R L ++ D + +R EE + LES D GKP +I + FF+ R + ++ Sbjct: 67 RQLALFRIADELEKRGEEFADLESQDAGKPRASLVEDEISLSVDQIRFFAGAARNLEGKS 126 Query: 133 T--QMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTA 190 M D ++ R P+GV+G + PWN PL + WK APA+AAGNT V+KP++ TP + Sbjct: 127 AGEYMKDHT-SFIRREPIGVVGQVAPWNYPLNMAVWKFAPAVAAGNTTVLKPSDTTPQST 185 Query: 191 TVLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKT 250 +LAEIC +P+GVVN++ G + G A+ +H +S TG G + +AA Sbjct: 186 LLLAEICA-MHLPEGVVNVITG--DRTTGGAMIDHKIPEMVSITGSVRAGLEVAKAAATD 242 Query: 251 LKRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAF--- 307 LKR+ ELGGK P ++F D+++ IE + + N G+ C +R+ V ++ F Sbjct: 243 LKRVHLELGGKAPVIVFDDADIPSAIEGIGIAGYFNAGQDCTAATRVVVHESIHDEFIAE 302 Query: 308 LEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEGLE 367 L+K+VA + G P D T G + + +RV G + + T+ GG R E Sbjct: 303 LKKWVAAN--VTTGLPSDPNTFYGPVNNANQMDRVMGILG-ELPSHSTVEAGGVRQG--E 357 Query: 368 KGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDL 427 +GYF+EPTI++GL ++ ++ EIFGPV+TV PF TEEE + N YGLS+SVWT D Sbjct: 358 RGYFIEPTIVSGLKQNDAAIQTEIFGPVITVQPFRTEEEAMTMANGVPYGLSSSVWTKDH 417 Query: 428 RRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNI 482 RA R A ++ G VW+N P GG K SG G++ + FE Y+ + ++ Sbjct: 418 ARAMRFAKGLDFGAVWINCHIPLVAEMPHGGFKHSGHGKDLSQYGFEEYTRVKHV 472 Lambda K H 0.318 0.136 0.404 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: 575 Number of extensions: 28 Number of successful extensions: 5 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: 478 Length adjustment: 34 Effective length of query: 452 Effective length of database: 444 Effective search space: 200688 Effective search space used: 200688 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 24 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