Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate WP_085218595.1 B9N75_RS09590 aldehyde dehydrogenase family protein
Query= BRENDA::Q88RC0 (480 letters) >NCBI__GCF_900177405.1:WP_085218595.1 Length = 479 Score = 262 bits (669), Expect = 2e-74 Identities = 169/457 (36%), Positives = 244/457 (53%), Gaps = 11/457 (2%) Query: 28 IKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTAKERSAKLRRWFELMIENQ 87 ++VT+ TG+V V + I AA KA + + ER A L+ + E Sbjct: 23 LEVTDKYTGKVAFRVAQADAKTIDAGIAAAVKAAEPMARMASYERQAVLQHCVDRFTERF 82 Query: 88 DDLARLMTTEQGKPLAEAKGEIAYAASFIEWFAEEAKRIYGDTIPGHQPDKRL-----IV 142 D+LA + E GKP+ +A+GE+ AEE+ R+ G+ P KR I Sbjct: 83 DELAYALCVEAGKPINDAEGEVTRLIDTFRIAAEESVRMTGEVQP-LDISKRARGYMGIW 141 Query: 143 IKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPYSALALVELAHRAGIP 202 + PIG + I+P+NFP + K PA+A GC V+KPAS+TP A+ + E+ +P Sbjct: 142 KRVPIGPCSFISPFNFPLNLAAHKIAPAIAVGCPFVMKPASRTPLGAIIMGEVLAETDLP 201 Query: 203 AGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLMEECAKDIKKVSLELGGNAPF 262 G S++ E T + ++ LSFTGS +G L + K KKV LELGGNA Sbjct: 202 KGAFSILPAHR-EGADMFTEDERLKLLSFTGSPGVGWDLKAKAGK--KKVVLELGGNAAV 258 Query: 263 IVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYDAFAEKLAAAVAKLKIGNGL 322 IV DADL+ AV I + +GQ+C+ RI + +YDA EKLAA L G+ Sbjct: 259 IVDKDADLEDAVARIIFGAFYQSGQSCIGVQRIIIHADIYDALKEKLAAKTKTLVAGDPH 318 Query: 323 EEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGKLIEGNFFEPTILVDVPKTAAVAK 382 + T GP+ID K ++ I++AV GAK+L GGK +G E T+L V ++A V + Sbjct: 319 DRKTFVGPMIDLKEATRLDNWIQEAVEGGAKLLVGGKR-DGAMLEATLLEGVDRSATVYR 377 Query: 383 EETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDMSRVFRVAEALEYGMVGIN-TG 441 EE FGP+A L +F D A + ND++FGL + + RD+ +V + L+ G V IN Sbjct: 378 EEAFGPVAILSKFDDFAAALDEVNDSKFGLQAGIFTRDIFQVLNAWDRLDVGGVVINDVP 437 Query: 442 LISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCI 478 + P+GG+K SGLGREG ++ +ED EI+ L I Sbjct: 438 SYRVDNMPYGGVKDSGLGREGIRFAMEDMTEIRNLVI 474 Lambda K H 0.317 0.134 0.384 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: 542 Number of extensions: 21 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: 480 Length of database: 479 Length adjustment: 34 Effective length of query: 446 Effective length of database: 445 Effective search space: 198470 Effective search space used: 198470 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: 51 (24.3 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