Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_013450164.1 CALNI_RS00150 aldehyde dehydrogenase
Query= BRENDA::Q9K9B2 (515 letters) >NCBI__GCF_000183405.1:WP_013450164.1 Length = 474 Score = 232 bits (592), Expect = 2e-65 Identities = 153/482 (31%), Positives = 251/482 (52%), Gaps = 27/482 (5%) Query: 39 LIINGERVTTEDKIQSWNPARKDQLVGSVSKANQDLAEKAIQSADEAFQTWRNVNPEERA 98 L I G+ V T I NP + L+ +S A+ + ++ I A ++ +ER Sbjct: 6 LFIEGKWVDTGKYIDVRNPY-DNSLIAQISMADAEWTDRGIDFAYSNRSIMASLTAKERG 64 Query: 99 NILVKAAAIIRRRKHEFSAWLVHEAGKPWKEADAD---TAEAIDFLEYYAR----QMIEL 151 +IL KA+ +I+ + + + E+GK + A + ++E F AR ++I L Sbjct: 65 DILNKASLLIKENLDDLAITIARESGKALRFAKGEVLRSSETFQFAADEARRLSGELIPL 124 Query: 152 NRGKEILSRPGEQNRYFYTPMGVTVTISPWNFALAIMVGTAVAPIVTGNTVVLKPASTTP 211 + +R G RY P+GV I+P+NF L ++ I GN +VLKPASTTP Sbjct: 125 DAAATGKNRFGYYKRY---PLGVIGAITPFNFPLNLVSHKVAPAIAAGNCIVLKPASTTP 181 Query: 212 VVAAKFVEVLEDAGLPKGVINYVPGSGAEVGDYLVDHPKTSLITFTGSKDVGVRLYERAA 271 + A K VE+L +AGLPK I + GSG+ VG+ +V+ + ++I+FTGS +VG+ + +A Sbjct: 182 LTAVKLVEILLEAGLPKEGITLLVGSGSSVGNRMVESDRLAMISFTGSPEVGLEIKRKAG 241 Query: 272 VVRPGQNHLKRVIVEMGGKDTVVVDRDADLDLAAESILVSAFGFSGQKCSAGSRAVIHKD 331 +K+V +E+G V++ +DAD+ A +V F SGQ C + R +H++ Sbjct: 242 --------MKKVTLELGNNSAVIIHKDADIASALPKCVVGGFANSGQVCISIQRIYVHRE 293 Query: 332 VYDEVLEKTVALAKNLTVGDPTNRDNYMGPVIDEKAFEKIMSYIEIGKKEG-RLMTGGEG 390 +YD + V KN + G + + +GP+I+EK ++ +I +G R+ GG+ Sbjct: 294 IYDLFTSQFVEAVKNTSYGSQLDENVVVGPMIEEKEAIRVEEWINEAVNQGARIACGGK- 352 Query: 391 DSSTGFFIQPTIIADLDPEAVIMQEEIFGPVVAFSKANDFDHALEIANNTEYGLTGAVIT 450 G ++PT++ D + ++ EEIFGPVV K + + A+E ANN++YGL + T Sbjct: 353 --RNGALLEPTVLLDTNETMKVVSEEIFGPVVCLMKYDTLEEAIEKANNSKYGLQAGIFT 410 Query: 451 RNRAHIEQAKREFHVGNLYFNRNCTGAIVGYHPFGGFKMSGTDSKAGGPDYLALHM-QAK 509 ++ A + VG + N T V P+GG K+SGT + GP + M + K Sbjct: 411 KDIKSAFDAIDKLEVGGVMVNDMPTFR-VDQMPYGGVKLSGTGRE--GPKFAVEEMTEIK 467 Query: 510 TV 511 TV Sbjct: 468 TV 469 Lambda K H 0.316 0.134 0.388 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: 558 Number of extensions: 28 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: 515 Length of database: 474 Length adjustment: 34 Effective length of query: 481 Effective length of database: 440 Effective search space: 211640 Effective search space used: 211640 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 (21.6 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