Align Aldehyde dehydrogenase family 2 member C4; ALDH1a; Protein REDUCED EPIDERMAL FLUORESCENCE 1; EC 1.2.1.3 (characterized)
to candidate WP_013450164.1 CALNI_RS00150 aldehyde dehydrogenase
Query= SwissProt::Q56YU0 (501 letters) >NCBI__GCF_000183405.1:WP_013450164.1 Length = 474 Score = 287 bits (735), Expect = 5e-82 Identities = 171/480 (35%), Positives = 275/480 (57%), Gaps = 16/480 (3%) Query: 21 KLFINGQFIDAASGKTFETIDPRNGEVIATIAEGDKEDVDLAVNAARYAFDHGPWPRMTG 80 KLFI G+++D +GK + +P + +IA I+ D E D ++ A Y+ + +T Sbjct: 5 KLFIEGKWVD--TGKYIDVRNPYDNSLIAQISMADAEWTDRGIDFA-YS-NRSIMASLTA 60 Query: 81 FERAKLINKFADLIEENIEELAKLDAVDGGKLFQLGKYADIPATAGHFRYNAGAADKIHG 140 ER ++NK + LI+EN+++LA A + GK + K ++ ++ F++ A A ++ G Sbjct: 61 KERGDILNKASLLIKENLDDLAITIARESGKALRFAK-GEVLRSSETFQFAADEARRLSG 119 Query: 141 ETLKM----TRQSLFGYTLKEPIGVVGNIIPWNFPSIMFATKVAPAMAAGCTMVVKPAEQ 196 E + + T ++ FGY + P+GV+G I P+NFP + + KVAPA+AAG +V+KPA Sbjct: 120 ELIPLDAAATGKNRFGYYKRYPLGVIGAITPFNFPLNLVSHKVAPAIAAGNCIVLKPAST 179 Query: 197 TSLSALFYAHLSKEAGIPDGVLNIVTGFGSTAGAAIASHMDVDKVSFTGSTDVGRKIMQA 256 T L+A+ + EAG+P + ++ G GS+ G + + +SFTGS +VG +I + Sbjct: 180 TPLTAVKLVEILLEAGLPKEGITLLVGSGSSVGNRMVESDRLAMISFTGSPEVGLEIKRK 239 Query: 257 AAASNLKKVSLELGGKSPLLIFNDADIDKAADLALLGCFYNKGEICVASSRVFVQEGIYD 316 A +KKV+LELG S ++I DADI A ++G F N G++C++ R++V IYD Sbjct: 240 A---GMKKVTLELGNNSAVIIHKDADIASALPKCVVGGFANSGQVCISIQRIYVHREIYD 296 Query: 317 KVVEKLVEKAKDWTVGDPFDSTARQGPQVDKRQFEKILSYIEHGKNEGATLLTGGKAIGD 376 + VE K+ + G D GP +++++ ++ +I N+GA + GGK Sbjct: 297 LFTSQFVEAVKNTSYGSQLDENVVVGPMIEEKEAIRVEEWINEAVNQGARIACGGKR--- 353 Query: 377 KGYFIQPTIFADVTEDMKIYQDEIFGPVMSLMKFKTVEEGIKCANNTKYGLAAGILSQDI 436 G ++PT+ D E MK+ +EIFGPV+ LMK+ T+EE I+ ANN+KYGL AGI ++DI Sbjct: 354 NGALLEPTVLLDTNETMKVVSEEIFGPVVCLMKYDTLEEAIEKANNSKYGLQAGIFTKDI 413 Query: 437 DLINTVSRSIKAGIIWVNCYFGFDLD-CPYGGYKMSGNCRESGMDALDNYLQTKSVVMPL 495 ++ G + VN F +D PYGG K+SG RE A++ + K+VV L Sbjct: 414 KSAFDAIDKLEVGGVMVNDMPTFRVDQMPYGGVKLSGTGREGPKFAVEEMTEIKTVVFNL 473 Lambda K H 0.318 0.136 0.402 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: 547 Number of extensions: 33 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: 501 Length of database: 474 Length adjustment: 34 Effective length of query: 467 Effective length of database: 440 Effective search space: 205480 Effective search space used: 205480 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