Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate 7023382 Shewana3_0612 succinylglutamic semialdehyde dehydrogenase (RefSeq)
Query= reanno::pseudo5_N2C3_1:AO356_23175 (500 letters) >FitnessBrowser__ANA3:7023382 Length = 487 Score = 167 bits (423), Expect = 8e-46 Identities = 149/468 (31%), Positives = 217/468 (46%), Gaps = 28/468 (5%) Query: 9 HYIDGRIQASDNARLSNVFNPATGAVQARVALAEPSTVDAAVASALAAFPAWSEQSSLRR 68 H+I G+ QA +++ NPA + R A V+AAV +A A W R Sbjct: 3 HFIKGQWQAGKGHDVTSS-NPANSEIIWRGQTATAEQVNAAVDAAREAQFDWFMLGFDGR 61 Query: 69 SRVMFKFKELLDRHHDELAQIISREHGKVLSDAHGEVTRGIEIVEYACGAPNLLK-TDFS 127 +++ ++ L+ + ELA+ I++E GK + EV I + + A N T+ + Sbjct: 62 LKIVEAYRSQLEANKAELAETIAQETGKPQWETATEVAAMIGKIGLSATAYNKRTGTEAN 121 Query: 128 DNIGGGIDNWNLR-QPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSERDPSASL 186 D G LR +P GV A P+NFP +P I AL+AGN + KPSE P + Sbjct: 122 DTPAGRAV---LRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSELTPKVAE 178 Query: 187 LMARLLTEAGLPDGVFNVVQGDKVAVDALLQHPDIEAISFVGSTPIAEYIHQQGTAQGKR 246 LM L +AGLP GV N+VQG+ AL HP ++ + F GS+ +HQQ + Sbjct: 179 LMVSLWEKAGLPAGVINLVQGEVDTGKALASHPQLDGLFFTGSSRTGHLLHQQYAGHPGK 238 Query: 247 VQALG-GAKNHMIVMPDADLDQAADALIGAAYGSAGERC-MAISIAVAVGDVGDELIAKL 304 + AL G N +I+ AD+ A ++ +AY S+G+RC A + V G+ GD L+AKL Sbjct: 239 ILALEMGGNNPLIIKGVADIKAAVHDILQSAYISSGQRCTCARRLYVEQGEQGDALVAKL 298 Query: 305 LPRIDQLKIGN-GQQPGTDMGPLVT-AEHKAKVEGFIDAGVAEGARLI-----VDGRGFK 357 + + Q+K+G QP MG +++ A K V + G L+ G G Sbjct: 299 VEAVKQIKVGPWNAQPQPFMGSMISEAAAKGMVAAQANLQNLGGVSLVELSHLQAGTGLV 358 Query: 358 VPGAEQGFFVGATLFDQVTAEMSIYQQEIFGPVLGIVRVPDFATAVALINAHEFGNGVSC 417 PG L D VTA + +E FGP+L +VR DF A+ L N +G Sbjct: 359 SPG----------LID-VTAVGELPDEEYFGPLLQLVRYSDFDQAIKLANQTRYGLSAGI 407 Query: 418 FTRDGGIARAFARSIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHA 465 F I+ G+V N I FGG S G+H A Sbjct: 408 LADSRDDYEYFLARIRAGIVNWNKQITGASGAAPFGGVGAS--GNHRA 453 Lambda K H 0.320 0.137 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: 516 Number of extensions: 21 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: 500 Length of database: 487 Length adjustment: 34 Effective length of query: 466 Effective length of database: 453 Effective search space: 211098 Effective search space used: 211098 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: 52 (24.6 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