Align Lmo2664 protein (characterized, see rationale)
to candidate CCNA_03124 CCNA_03124 NAD/mycothiol-dependent formaldehyde dehydrogenase
Query= uniprot:Q8Y413 (350 letters) >FitnessBrowser__Caulo:CCNA_03124 Length = 366 Score = 128 bits (321), Expect = 3e-34 Identities = 107/358 (29%), Positives = 164/358 (45%), Gaps = 36/358 (10%) Query: 1 MRAAVLYENNVIKAEQIDEATCGKD---QVRVEVKAVGICGSDIHKMQTRWKYPLPAVMG 57 M+AAVL E V K QI+ GK +V + KA G+C SD+H ++ + + LPAV+G Sbjct: 1 MKAAVLRE--VGKPLQIETVAIGKPGPREVLIRTKAAGVCHSDLHFVEGSYTHALPAVLG 58 Query: 58 HEFAGVITEIGSEVTNVAMGDRVAGIPLEPCMECNYCKAGDFALC----------DNYRM 107 HE AG++ +GSEV V +GD V C C C G LC D R+ Sbjct: 59 HESAGIVEAVGSEVRTVKVGDHVITCLNPYCGHCEVCLTGHMNLCISPETRRSKSDAPRL 118 Query: 108 VGSHFHG------------GFAENVVMKADNVISI-GDLDFEEGAMIEPLAVSMHGVL-- 152 +G FAE +++ ++I D+ F+ A+I ++ G + Sbjct: 119 FKEDLNGATGPMAQFLNLSSFAEMMLVHEHACVAIRKDMPFDRAALIGCSVMTGVGAVMH 178 Query: 153 GIQPRLGDTVIVFGIGTIGILVVQCLLLAGVKDIIAVDISDKKLADAREFGCKYTINPKN 212 R G+TV V G G +G+ + +AG IIA+D KL A+ FG ++ Sbjct: 179 TSNVRPGETVAVIGCGGVGLATINGAAIAGAGRIIAIDRLAGKLELAKTFGATDVVDASQ 238 Query: 213 -EDLKERVFAYTNGLGADIALECAGSKITQEQCLLVTKKKGKVGFLGIAYADVLLHEEAF 271 +D+ + V T G G + E G K T E + ++ G +G+ + Sbjct: 239 VDDIAKAVVELTGG-GVHHSFEAIGLKATAEASFKMLRRGGTANVIGMIPVGTKIELHGV 297 Query: 272 ENIFRRELTLKGFWNSYSAPFPGEEWRTSIEFVKQGRIKLKPLISHRYKLEETKEAFD 329 + F E ++G + S FP + R ++F G++KL LIS R KLE+ AFD Sbjct: 298 D--FLGERRIQGSYMG-SNRFPVDMPRL-VDFYMSGKLKLDELISRRIKLEDVNSAFD 351 Lambda K H 0.321 0.139 0.417 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: 286 Number of extensions: 16 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: 350 Length of database: 366 Length adjustment: 29 Effective length of query: 321 Effective length of database: 337 Effective search space: 108177 Effective search space used: 108177 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: 49 (23.5 bits)
This GapMind analysis is from Sep 17 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