Align Putative aldehyde dehydrogenase YwdH; EC 1.2.1.3 (uncharacterized)
to candidate WP_019866236.1 METMI_RS25445 MFS transporter
Query= curated2:P39616 (456 letters) >NCBI__GCF_000384075.1:WP_019866236.1 Length = 935 Score = 399 bits (1026), Expect = e-115 Identities = 205/440 (46%), Positives = 286/440 (65%), Gaps = 1/440 (0%) Query: 16 AAGHTRPLESRLNILRKLKQAVRTHEADLIAALYQDLHKSEQEAYSTEIGIVLEEISFVM 75 A+G TRP R LR L + + +E + AL QDL K EAY +EI V EE+ + Sbjct: 496 ASGKTRPTRFRKAALRDLLRIIEENEGLMFDALRQDLGKPAMEAYMSEIFCVKEELRLSL 555 Query: 76 KRLRKWSKPKRVKTPLTHLGSKSIIIPEPYGTVLVIAPWNYPLQLALSPLIGAIAAGNTV 135 K+L W++ + V TP ++S I P+GTVLV+ PWNYPLQLAL PL+ A+AAGNTV Sbjct: 556 KKLDAWARDEAVATPWWLWPARSWIRKVPFGTVLVLVPWNYPLQLALMPLVAALAAGNTV 615 Query: 136 VLKPSEYTPAVSAILSKLISSVFPTDYVAMAEGGPDVSTALLQQPFDYIFFTGSVAVGKI 195 V+KPSE PA SA+L + I+ +F V++ GG D + +LL+QPFD+ FFTG +G+ Sbjct: 616 VIKPSELAPA-SAVLLQAIARLFEPGLVSVVNGGADTARSLLEQPFDFFFFTGGAEIGRQ 674 Query: 196 VMEAAAKQLIPVTLELGGKSPCIVHKDADIQLAAKRIVFGKFTNAGQTCIAPDYLFVHED 255 V AA + IP LELGGK+PCIV + A + LAA+RIV+GKF NAGQTC+APD+++VH D Sbjct: 675 VALKAAAKGIPCVLELGGKNPCIVDESAPLALAARRIVWGKFFNAGQTCLAPDHVYVHRD 734 Query: 256 IKTKLTEEMKRAIREFYGPQPERNPQYGKIVSERHYQRLLSFLNDGIPLTGGQSDPNHHK 315 + L EM + + +FYG QP +P +IV+ RH+ RLL +L +G GG+ D + + Sbjct: 735 VYEALLLEMAKVVGDFYGGQPWLSPDLAQIVNVRHFARLLGYLEEGRVAHGGRYDTDARR 794 Query: 316 IAPTILEQVRDDSPVMQEEIFGPILPLFTYRNIGEVIEKVQSRPKPLALYLFTTNKEIER 375 I PT+L + ++ VM+EEIFGPILP+ Y ++ +++ +QS+P PLA+YL T ++ E Sbjct: 795 IGPTLLVDIVPNAAVMREEIFGPILPVLPYDDLSVLLDTLQSQPVPLAMYLHTRRRDTEA 854 Query: 376 AVLGNLSFGGGCVNDTLMHVATPYLPFGGVGESGIGSYHGFDSFNTFTHKKSVVKQTNRF 435 VL G CVND LM P LPFGG+ SGIG YHG F+TFTH ++V++Q+ R+ Sbjct: 855 LVLQRTRSGSVCVNDHLMQAGVPALPFGGMAHSGIGRYHGRHGFDTFTHARAVLRQSTRW 914 Query: 436 DFAFRYPSSKNGLRMIRKIL 455 D RYP L +R++L Sbjct: 915 DNHLRYPPGDAKLVWLRRLL 934 Lambda K H 0.320 0.137 0.401 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: 946 Number of extensions: 41 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: 456 Length of database: 935 Length adjustment: 38 Effective length of query: 418 Effective length of database: 897 Effective search space: 374946 Effective search space used: 374946 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 (21.8 bits) S2: 54 (25.4 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