Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate WP_110208307.1 DNK54_RS17595 aldehyde dehydrogenase family protein
Query= BRENDA::P23883 (495 letters) >NCBI__GCF_003194585.1:WP_110208307.1 Length = 492 Score = 409 bits (1052), Expect = e-119 Identities = 222/484 (45%), Positives = 305/484 (63%), Gaps = 11/484 (2%) Query: 18 IENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSL 77 ++ +LFI GE+ AA+ TFET+DP LA +A ++ D+DRA++AA F WS Sbjct: 1 MQQKLFIGGEFVDAADGGTFETIDPHDGTVLANVAEARAADVDRAVAAAASAFPA--WSR 58 Query: 78 SSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDK 137 + A R +L +LAD +E + LALLET DTG P+R + D+P A R++ DK Sbjct: 59 MAAADRGRLLLRLADAIEDDVDALALLETRDTGHPVRDTRGLDVPRTAATFRYFGGMADK 118 Query: 138 VYGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSP 197 G V L +V EP+GV+ IVPWNFP++ T WK+GPALAAGN V++KPSE SP Sbjct: 119 FQGSVVPVEQGFLDYVVPEPLGVVGQIVPWNFPVMFTSWKMGPALAAGNCVVMKPSEISP 178 Query: 198 LSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAG 257 LSA+R+A LA E G P GV+N+V GFG AG + H I I+FTGST G+ + + A Sbjct: 179 LSALRVAELAAEVGFPPGVINMVPGFGATAGARIVDHPAIAKISFTGSTAVGQSIARSAA 238 Query: 258 DSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADE 317 DS +K+V LE GGK ANIVF D D+ A + TA GIF+NQGQ CIA +RL++ E++ DE Sbjct: 239 DS-LKQVHLELGGKGANIVFDDA-DMAAAVNGTAFGIFHNQGQACIAASRLIVHEAVKDE 296 Query: 318 FLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRNAGLAA 377 FL L ++ + G P DPAT MG L H D V S + E +G +L G +A Sbjct: 297 FLERLITLTRSIRLGDPKDPATEMGPLTSSQHRDRVMSHLALTEEEGGTVLTGGHAPQDR 356 Query: 378 AIG------PTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWT 431 A+ PTI V+ P++ ++EE+FGP +VV F +E++AL++AND YGLG +WT Sbjct: 357 ALADGFYVEPTI-VETVPDSRAAQEEVFGPFMVVHAFKTEDEALRIANDVAYGLGGGLWT 415 Query: 432 RDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWI 491 RDLSRAHR++R L+AG V+VN+Y + PFGG SG GR+ A+ ++T K WI Sbjct: 416 RDLSRAHRVARDLRAGMVWVNSYKRVNPGSPFGGVGVSGYGREMGFEAMREYTSPKATWI 475 Query: 492 SLEA 495 +++A Sbjct: 476 NIDA 479 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: 608 Number of extensions: 29 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: 495 Length of database: 492 Length adjustment: 34 Effective length of query: 461 Effective length of database: 458 Effective search space: 211138 Effective search space used: 211138 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