Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate WP_108359063.1 B9Z44_RS11550 aldehyde dehydrogenase family protein
Query= BRENDA::P23883 (495 letters) >NCBI__GCF_003063475.1:WP_108359063.1 Length = 477 Score = 313 bits (802), Expect = 8e-90 Identities = 182/475 (38%), Positives = 274/475 (57%), Gaps = 11/475 (2%) Query: 21 RLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSP 80 ++FING+ A + + + PV +I RG+ D+D A++AA + W + Sbjct: 3 KMFINGQSVNALSGKVLDVLSPVDGQKFEEIPRGEKADVDLAVNAANKALDSA-WGKMTA 61 Query: 81 AKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYG 140 +R +L KL + + H ELA LE DTGKP+ + + DI AR +Y DK++G Sbjct: 62 LERGRLLMKLGEKVLEHHAELAALEARDTGKPMT-TAKTDITVLARYFEFYGSGADKIHG 120 Query: 141 EVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSA 200 V ++REP+GV A I+PWN+P + + PALA GN+V++KP+E + L+ Sbjct: 121 LVLPFLDGYTVNVLREPLGVTAHIIPWNYPAQMLGRSIAPALAMGNAVVVKPAEDACLTP 180 Query: 201 IRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSN 260 IR+A LA++ G PDG +N+VTG G EAG ALS H I+ I+FTGS G L++ A N Sbjct: 181 IRVAELARDVGFPDGAINIVTGLGEEAGAALSEHPGINFISFTGSNEVG-VLIQKAAAKN 239 Query: 261 MKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLA 320 + + LE GGKS ++VF D DL +A GI N GQ C AG+RL++++SI E + Sbjct: 240 VIKCVLELGGKSPHVVFGDA-DLDRAVPIITRGIIANTGQTCTAGSRLIVQKSIYPEIME 298 Query: 321 LLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKG-QLLLDG-RNAGLAAA 378 L +Q + G P D G +++ A D V F++E E G +++ G + GL Sbjct: 299 RLAKQFAQIKVGTP-DMDLDCGPVVNIAQRDRVAYFLKEAEKSGIEMVAQGVLSPGLPKE 357 Query: 379 ---IGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDLS 435 + PT+ +V N ++EEIFGPVL F +E + + LAN + +GL AAVWT + Sbjct: 358 GYYVTPTLLGNVPANHRCAQEEIFGPVLAAMSFDTEAEGIALANGTDFGLMAAVWTENGG 417 Query: 436 RAHRMSRRLKAGSVFVNNYN-DGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTI 489 R R+S+ +KAG V++N + G + +PFGG K+SG+GR+K ALE+ + KT+ Sbjct: 418 RQQRVSKAIKAGQVYINAFGAGGGVELPFGGVKRSGHGREKGFLALEEVSTTKTV 472 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: 554 Number of extensions: 25 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: 477 Length adjustment: 34 Effective length of query: 461 Effective length of database: 443 Effective search space: 204223 Effective search space used: 204223 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 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