Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_011372957.1 SUDEN_RS06940 1-pyrroline-5-carboxylate dehydrogenase
Query= BRENDA::Q9RW56 (523 letters) >NCBI__GCF_000012965.1:WP_011372957.1 Length = 1182 Score = 222 bits (565), Expect = 7e-62 Identities = 165/521 (31%), Positives = 264/521 (50%), Gaps = 41/521 (7%) Query: 7 YRPQPFTDFTKEENVQAYQAALAKVRKEL--LGKHYPL----IIDGQEVDTEGKIQSINP 60 ++ + TDFT +N Q K+R + + K PL ++ G+E+ ++ +++ + Sbjct: 476 FKNESDTDFTLTQN----QIWADKIRDKYKNISKEEPLRVHIVVGGKELMSQ-EVKEVMD 530 Query: 61 CDTSEVVGTTAKATIGDAENALQGAWKAFESWKKWDMDARARILLKAAAILKRRRLEACA 120 + + A + A++ A ++W + + R ++L+ A ++ R Sbjct: 531 KSQNITLHRCFMAGEDVLKEAIEVAKSDVDAWSELTLKERTKVLMNVANEFRKNRGLLIG 590 Query: 121 LMSIEVGKNYAEADVEVAEAIDFLEYYARSAMKYAGFGSSETTWFEGEENGLMSIPLGVG 180 + + E+GK ++E+DVE++EAIDFL +Y S K E +G+ GVG Sbjct: 591 IAAAELGKIFSESDVEISEAIDFLNFYPYSLKKL------------NELDGIKLEEKGVG 638 Query: 181 VSISPWNFPCAIFVGMAAAPIVAGNCVVVKPAEDAGLIAGFMVDILREAGLPAGVLQFLP 240 + ISPWNFP AI VG AA + GN V++KP+ DA L + +AG+ LQF+P Sbjct: 639 LVISPWNFPIAIAVGGVAAALACGNRVILKPSSDALLCGYMLCKCFWDAGVSKNTLQFIP 698 Query: 241 GVGKEVGEYLTTHAKTRFITFTGSRAVGLHINEVAAKVQPGQKWIKRVIMELGGKDGLIV 300 G+ GE+L F+ FTGS + A K+ + I + E GGKD IV Sbjct: 699 TQGELAGEFLLKSKDIDFVIFTGS-------EKTAYKMLKNRPEI-HLSAETGGKDATIV 750 Query: 301 DETADIENAITAATQGAFGFNGQKCSAMSRLIVVDSVY--DEVVNGFVERAKALKMGTGE 358 +D + AI AF +GQKCSA S LI+ VY +E ++ +L +G+ Sbjct: 751 TALSDRDQAIKNVVASAFNNSGQKCSATSLLILEREVYEDEEFKKMLIDATLSLHVGSVW 810 Query: 359 ENAN-VTAVVNQMSFNKIKGYLELAPSEGKVLLGGEATGEANGKQGYYIQPTIVGDVDRN 417 + N ++++VN S N +K LE +G+ L + ++N Y ++P+I + Sbjct: 811 DTQNRISSLVNIPSGN-LKYALEHL-DDGEEWLIAPSFEDSN---PYMLKPSIRWGTKKG 865 Query: 418 SRLAQEEIFGPVVAVLRAKDWQDALDIANSTEYGLTGGVCSNSRERLEQARAEFEVGNLY 477 E+FGPV++V+ A+D DAL + NST YGLT G+ S + + + GNLY Sbjct: 866 DFCHMNELFGPVLSVMCAEDLDDALSLVNSTGYGLTSGIESLDEREVLKFKENLMAGNLY 925 Query: 478 FNRKITGAIVGVQPFGGYNMS--GTDSKAGGPDYLSNFMQL 516 NR TGA+V QPFGG S G+ KAGG +Y+S F+ + Sbjct: 926 INRMTTGAVVLRQPFGGMGKSAIGSGKKAGGFNYVSQFVNI 966 Lambda K H 0.317 0.134 0.391 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: 1144 Number of extensions: 45 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: 523 Length of database: 1182 Length adjustment: 41 Effective length of query: 482 Effective length of database: 1141 Effective search space: 549962 Effective search space used: 549962 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: 55 (25.8 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