Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_022599797.1 NSB1T_RS16830 aldehyde dehydrogenase
Query= BRENDA::Q8BH00 (487 letters) >NCBI__GCF_000473955.1:WP_022599797.1 Length = 455 Score = 145 bits (367), Expect = 2e-39 Identities = 109/342 (31%), Positives = 164/342 (47%), Gaps = 19/342 (5%) Query: 144 PVGIAGLISPWNLPLYLLTWKIAPAIAAGNTVIAKPSEMTSVTAWMFCKLLDKAGVPPGV 203 P GI+ ++SPWN P LL + A+AAGN VI KPS + T + K++ +A P V Sbjct: 103 PYGISLILSPWNYPFQLLFAPLIGAVAAGNCVILKPSPASPHTTAVSKKIIKEAFDPCHV 162 Query: 204 INIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAPHCKKLSLELGGKNPAIIF 263 I I L+ I +TG +R+ + ++ H ++LELGGK+P II Sbjct: 163 ILI---EADNRETDLLLQQRYDYIFYTGGVEYGKRVMEAASKHLTPVTLELGGKSPCIID 219 Query: 264 EDANLEECIPATVRSSFANQGEICLCTSRIFVQRSIYSEFLKRFVEATRKWKVGVPSDPS 323 +DAN++ V F N G+ C+ IFV + I ++ + + + + + G S Sbjct: 220 KDANIDIAARRIVWGKFLNCGQTCVAPDYIFVHQDIKNDLILKLKDEIIR-QYGKDPQKS 278 Query: 324 ANMGALISKAHLEKVRSYVLKAQTEGARILCGEGVDQLSLPLRNQAGYFMLPTVITDIKD 383 + +I R Y L + +I G D+ L ++ PTVI+ I Sbjct: 279 PDYPRIIHSG-----RFYNLMLLLKQGKIEAGGKYDEKDL--------YIAPTVISGITP 325 Query: 384 ESRCMTEEIFGPVTCVVPFDSEEEVITRANSVRYGLAATVWSKDVGRIHRVAKKLQSGLV 443 E+R M EEIFGP+ V+ F+ E VI NS LA + K+ I + +K SG V Sbjct: 326 ENRIMNEEIFGPILPVMTFNERETVIDYINSQEKPLALYYFGKNKKNIREILEKTSSGGV 385 Query: 444 WTNCWLIRELN--LPFGGMKSSGIGREGAKDSYDFFTEIKTI 483 N + N LPFGG+ SGIGR DS+ F+ K++ Sbjct: 386 CINDVVTHLANPDLPFGGVGHSGIGRYHGIDSFYTFSHTKSV 427 Lambda K H 0.319 0.134 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: 491 Number of extensions: 26 Number of successful extensions: 4 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: 487 Length of database: 455 Length adjustment: 33 Effective length of query: 454 Effective length of database: 422 Effective search space: 191588 Effective search space used: 191588 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: 51 (24.3 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