Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate CCNA_03243 CCNA_03243 NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__Caulo:CCNA_03243 Length = 499 Score = 470 bits (1210), Expect = e-137 Identities = 245/487 (50%), Positives = 336/487 (68%), Gaps = 4/487 (0%) Query: 11 DKALSLAIENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVF 70 ++ LA ++ I+G+ AA TF V P L + ++ D++RA++ AR F Sbjct: 12 ERLAKLAPPSQAVIDGDLVEAASGATFHNVSPRDGQVLNLVTACQADDVERAVAGARAAF 71 Query: 71 ERGDWSLSSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRW 130 E G W P ++KAVL +LA+LME A+ELALLE+LD GKPI + DIP A RW Sbjct: 72 EDGRWRDQGPRQKKAVLFRLAELMERDADELALLESLDVGKPISDARNVDIPLAINTCRW 131 Query: 131 YAEAIDKVYGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVIL 190 YAEA+DKVYGEV T+ + L+ V EP+GVI AIVPWNFPL + WK+ PALA GNSV+L Sbjct: 132 YAEALDKVYGEVGTSPADRLSYAVHEPLGVIGAIVPWNFPLHMAMWKVAPALAMGNSVVL 191 Query: 191 KPSEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGK 250 KP+E+SPL+A++L LA EAGLP GVLNV+ G G AG+AL+ D+D IAFTGS G+ Sbjct: 192 KPAEQSPLTALKLGALALEAGLPPGVLNVIPGLGGVAGEALALSMDVDMIAFTGSGPVGR 251 Query: 251 QLLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLL 310 +L++ + SN+KRV LE GGKS IVFADCPDL+ AA A A G+FYNQG+VC A +RLL+ Sbjct: 252 RLMEYSARSNLKRVSLELGGKSPQIVFADCPDLEAAAQAAAWGVFYNQGEVCTAASRLLV 311 Query: 311 EESIADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKG-QLLLD 369 E I D FLA + + A+ + G PLDP+T G ++ ++ +I +S+G + +L Sbjct: 312 EAPIKDAFLARVIEVAKGMKVGDPLDPSTQFGAMVSERQMNTALDYIATADSQGARRVLG 371 Query: 370 GRNAGLAAA---IGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLG 426 G+ A + PTIF V P+ +L+REE+FGPVL V F+SE++A++LAND+ YGL Sbjct: 372 GQRVRQEAGGFYVEPTIFDQVRPDQTLAREEVFGPVLGVMTFSSEDEAMRLANDTVYGLA 431 Query: 427 AAVWTRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTEL 486 A +WT D+S+A R +RRLKAG V+VN ++ D+T+PFGG+KQSG GRD+SLHAL K+ +L Sbjct: 432 AGLWTADVSKALRGARRLKAGLVWVNGWDACDITMPFGGFKQSGFGRDRSLHALHKYADL 491 Query: 487 KTIWISL 493 K++ ++L Sbjct: 492 KSVSVTL 498 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: 603 Number of extensions: 22 Number of successful extensions: 2 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