Align Putative aldehyde dehydrogenase AldA; EC 1.2.1.3 (uncharacterized)
to candidate WP_009488515.1 C683_RS01225 NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
Query= curated2:Q2YV11 (495 letters) >NCBI__GCF_000313915.1:WP_009488515.1 Length = 473 Score = 235 bits (600), Expect = 2e-66 Identities = 160/489 (32%), Positives = 266/489 (54%), Gaps = 31/489 (6%) Query: 11 ENYGLFINGEFVKGSSDETIEVTNPATGETLSHITRAKDKDVDHAVEVAQEAFESWSLTS 70 ++Y +NGE+ KG+S +TI + PATG+ L + ++K+++ ++ A++A + W + Sbjct: 2 KSYLNLVNGEW-KGTS-QTITIKEPATGKELGTVPAMEEKEIEEVMQSARQAQKEWQALA 59 Query: 71 KSERAQMLRDIGDKLMAQKDKIAMIETLNNGKPIRETTAIDIPFAARHFHYFASVIET-- 128 ERAQ+L L + +I + + K I ++ A I R A E Sbjct: 60 VVERAQILHQAAQLLKKEAVEIGTLLS----KEIAKSRAASIQEVERTADLIAYTAEEGC 115 Query: 129 -------EEGTVNDIDKDTMSIVRHEPIGVVGAVVAWNFPMLLAAWKIAPAIAAGNTIVI 181 E G+ + D++ ++ V E +GVV A+ +N+P+ LAA KIAPA+ GNT+V Sbjct: 116 RMEGQILEGGSFSKKDQNKIAFVHKEAMGVVLAIAPFNYPVNLAASKIAPALIGGNTVVF 175 Query: 182 QPSSSTPLSLLEVAKIFQEV-LPKGVVNILTGKGSESGNAIFNHDGVDKLSFTGSTDVGY 240 + + +S L++A+IF E +P GV+N +TG+GS G+A+ H VD ++FTGST++G Sbjct: 176 KTPTQGAISGLQLARIFHEAGVPAGVLNTVTGRGSVIGDALVTHPEVDAINFTGSTEIGT 235 Query: 241 QVAEAAAKHLVPATLELGGKSANIILDDANLDLAVEGIQLGILFNQGEVCSAGSRLLVHE 300 +AE A + P +ELGGK A ++L+DA+L+ A + I G G+ C+A R+ V E Sbjct: 236 HIAELAG--MKPCIMELGGKDAALVLEDADLENAAKEIVAGAFQYSGQRCTAIKRVFVTE 293 Query: 301 KIYDQLVPRLQEAFSNIKVGDPQDEATQMGSQTGKDQLDKIQSYIDVAKESDAQILAGGH 360 K D LV +Q+ + VG P++ A + + D I+ I+ A +L G Sbjct: 294 KNADALVAAIQKEMETLSVGLPEENA-DITPLIDRFVADHIEFLIEDA------LLKGAV 346 Query: 361 RLTENGLDKGFFFEPTLIAVPDNHHKLAQEEIFGPVLTVIKVKDDQEAIDIANDSKYGLA 420 T+ ++ + P L+ LA EE FGPVL +++VKD +E I +AN S+YGL Sbjct: 347 AKTKYQRERNLIW-PMLLDQVTVDMDLAWEEPFGPVLPILRVKDVEEMIRLANASEYGLQ 405 Query: 421 GGVFSQNITRALNIAKAVRTGRIWINTYNQVPEGA---PFGGYKKSGIGRETYKGALSNY 477 +F+ N A+ I KA++ G + +N ++ GA PF G K SG+G + K ++ Sbjct: 406 SAIFTNNYPLAMEIGKALKVGTVHMN--HRTQRGADHFPFLGIKNSGLGVQGIKYSIDAM 463 Query: 478 QQVKNIYID 486 ++K+ + Sbjct: 464 MRMKSFVFE 472 Lambda K H 0.315 0.133 0.377 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: 488 Number of extensions: 34 Number of successful extensions: 6 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: 495 Length of database: 473 Length adjustment: 34 Effective length of query: 461 Effective length of database: 439 Effective search space: 202379 Effective search space used: 202379 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: 42 (22.0 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