Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate WP_011383257.1 AMB_RS04160 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P23883 (495 letters) >NCBI__GCF_000009985.1:WP_011383257.1 Length = 499 Score = 288 bits (738), Expect = 2e-82 Identities = 173/481 (35%), Positives = 266/481 (55%), Gaps = 15/481 (3%) Query: 18 IENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSL 77 I++ +++G + A + F+ +DP T +A + + + RA+ AA + W Sbjct: 23 IKSHAYVDGVWVGADDGRRFDVLDPATGGLIASVPDLGATETRRAIDAAEAAWN--PWRQ 80 Query: 78 SSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDK 137 + R AV+ DL+ AH + LA L + + GKP+ ++ +I A I W+AE + Sbjct: 81 RTAKDRAAVMMAWHDLIMAHQDALARLLSAEQGKPLAEAM-GEISYGASFISWFAEEGKR 139 Query: 138 VYGE-VATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKS 196 YG+ + TT+S +++++P+GV+AA+ PWNFP+ + K PALAAG V++KP+E + Sbjct: 140 AYGDLIPTTASDRRLLVMKQPIGVVAAVTPWNFPMAMITRKCAPALAAGCPVVVKPAEDT 199 Query: 197 PLSAIRLAGLAKEAGLPDGVLNVVTGFGHEA-GQALSRHNDIDAIAFTGSTRTGKQLLKD 255 PLSA+ LA LA AGLP G+ N+VT A G ++ + + ++FTGSTR GK L+ Sbjct: 200 PLSALALAELAHRAGLPKGLFNIVTTRQPAAVGGEMTGNAKVRKLSFTGSTRVGKLLMAQ 259 Query: 256 AGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIA 315 ++ +K+V LE GG + IVF DC DL A + A + N GQ CI R L++ I Sbjct: 260 CAET-VKKVSLELGGNAPFIVFDDC-DLDAAVAGALASKYRNSGQTCICTNRFLVQAGIY 317 Query: 316 DEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRNAGL 375 ++F L ++A GH L G LI+ A V + + + SKG +L G G Sbjct: 318 EDFAVKLAEKAAAMAVGHALSGVVQQGPLINAAAVAKVAAHVADAVSKGARVLTG---GR 374 Query: 376 AAAIG-----PTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVW 430 A+G PT+ DV P REE FGPV + RF +E +A+ LAN S++GL + Sbjct: 375 PHALGGGFWQPTVLADVTPAMLCFREETFGPVAPLLRFETEAEAIALANASEFGLAGYFY 434 Query: 431 TRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIW 490 +RD++R R++ L+ G V VN + PFGG K+SG GR+ S + L+ F E K + Sbjct: 435 SRDVARVFRVAEALECGMVGVNESLISNEVAPFGGIKESGLGREGSKYGLDDFMETKYVC 494 Query: 491 I 491 I Sbjct: 495 I 495 Lambda K H 0.317 0.133 0.389 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: 573 Number of extensions: 28 Number of successful extensions: 7 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: 499 Length adjustment: 34 Effective length of query: 461 Effective length of database: 465 Effective search space: 214365 Effective search space used: 214365 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 (21.7 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