Align Aldehyde dehydrogenase (EC 1.2.1.3) (characterized)
to candidate WP_012536996.1 AFE_RS09825 aldehyde dehydrogenase family protein
Query= reanno::Marino:GFF3202 (533 letters) >NCBI__GCF_000021485.1:WP_012536996.1 Length = 506 Score = 817 bits (2111), Expect = 0.0 Identities = 392/506 (77%), Positives = 441/506 (87%) Query: 28 MIYAQPGKDGSVVSFKSRYENYIGGEWVAPVKGQYFENITPVTGNVICEIPRSSAEDIDL 87 M YA P +G+VV+FK RY+N+IGG WVAPV+G+YF+NI+P+ G C+IPRSSAEDI+L Sbjct: 1 MQYANPNTEGAVVNFKERYDNFIGGRWVAPVRGEYFDNISPINGKPFCQIPRSSAEDIEL 60 Query: 88 ALDAAHKAAPAWGKTSPTERSNILLKIADRIEANLEKLAVAETWDNGKAVRETLNADIPL 147 ALDAAH A AWG+TS T RSNILLKIADRI+ANLE LAVAETWDNGKAVRETLNAD+PL Sbjct: 61 ALDAAHAAKDAWGRTSVTARSNILLKIADRIDANLEMLAVAETWDNGKAVRETLNADVPL 120 Query: 148 AADHFRYFAGCLRAQEGHMGEIDHNTVAYHFHEPLGVVGQIIPWNFPILMAAWKLGPCLA 207 ++DHFRYFAGCLRAQEG +GEID NTVAYHFHEPLGVVGQIIPWNFP+LMA WKL P LA Sbjct: 121 SSDHFRYFAGCLRAQEGTIGEIDENTVAYHFHEPLGVVGQIIPWNFPLLMACWKLAPALA 180 Query: 208 AGNCTVLKPAEQTPASILVLMEIIGDLLPPGVLNIVNGYGIEAGQALATSKRIAKIAFTG 267 AGNC VLKPAEQTPASILV+ME+I DLLP GVLN+VNGYG+EAG+ALATSKRIAKIAFTG Sbjct: 181 AGNCVVLKPAEQTPASILVMMELIADLLPAGVLNVVNGYGVEAGKALATSKRIAKIAFTG 240 Query: 268 STPVGSHILKCAAENIIPSTVELGGKSPNIYFSDVMKAEPEFIDKCVEGLVLAFFNQGEV 327 STPVGS I+K AAENIIPSTVELGGKSPNI+F+DV+ E F+ K VEG VLAFFNQGEV Sbjct: 241 STPVGSLIMKYAAENIIPSTVELGGKSPNIFFADVLDQEDAFVSKAVEGAVLAFFNQGEV 300 Query: 328 CTCPSRALVQEDMFEEFMQKVVQRTKSIKRGNPLDTDVQVGAQASKEQFDKIMSYLAIGK 387 CTCPSR L+QE ++E+F+ VV+R+ IKRGNPLDT+V VGAQAS+EQ+DKI+SY+ IGK Sbjct: 301 CTCPSRLLIQESIYEKFIGMVVERSAQIKRGNPLDTEVMVGAQASQEQYDKILSYIQIGK 360 Query: 388 EEGAVVLTGGDREHLDEEFNNGFYIQPTLFKGDNKMRVFQEEIFGPVVGVTTFKTEEEAL 447 +EGA V+TGG E + ++ G+YIQPTL KG N MRVFQEEIFGPVV VTTFK E EAL Sbjct: 361 DEGAEVITGGAVETMSADYCEGYYIQPTLLKGTNNMRVFQEEIFGPVVSVTTFKDEAEAL 420 Query: 448 AIANDTEFGLGAGVWTRDTNLAYRMGRNIQAGRVWMNCYHAYPAHAAFGGYKKSGVGRET 507 AIAND EFGLGAGVWTRD N AYRMGR IQAGRVW NCYH YPAHAAFGGYKKSGVGRET Sbjct: 421 AIANDIEFGLGAGVWTRDMNRAYRMGRGIQAGRVWTNCYHMYPAHAAFGGYKKSGVGRET 480 Query: 508 HKMALEHYQQTKCMLTSYDTNPLGFF 533 HKM L+HYQQTK +L SYD NPLGFF Sbjct: 481 HKMMLDHYQQTKNLLVSYDINPLGFF 506 Lambda K H 0.319 0.136 0.412 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: 868 Number of extensions: 34 Number of successful extensions: 1 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: 533 Length of database: 506 Length adjustment: 35 Effective length of query: 498 Effective length of database: 471 Effective search space: 234558 Effective search space used: 234558 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