Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_092345688.1 BLU87_RS05845 aldehyde dehydrogenase family protein
Query= reanno::WCS417:GFF827 (481 letters) >NCBI__GCF_900107645.1:WP_092345688.1 Length = 477 Score = 624 bits (1609), Expect = 0.0 Identities = 305/472 (64%), Positives = 370/472 (78%) Query: 9 NYINGQWVAGADYCVNLNPSELSDVIGEYAKADVTQVNAAIDAARAAFPAWSTSGIQARH 68 NYING+WV D +++NPS+ +D+IGEYA+AD Q N AI AA+AA W + + Sbjct: 6 NYINGEWVESNDVNLDINPSDTNDIIGEYARADEQQTNDAIQAAKAARNVWRDVCVNEKS 65 Query: 69 DALDKVGSEILARREELGTLLAREEGKTLPEAIGEVTRAGNIFKFFAGECLRLSGDYVPS 128 LD +GSEILAR+ EL TLLAREEGKTLPEA GEV RAG IFKFF+GE +RL+GD + S Sbjct: 66 IILDNIGSEILARKTELATLLAREEGKTLPEATGEVVRAGMIFKFFSGEAVRLTGDILAS 125 Query: 129 VRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVIKPAELVPGCAWALA 188 RPG+NVE+TRE +GV+G+I+PWNFPIAIPAWKIAPALA+GN VV+K A+LVP AWALA Sbjct: 126 TRPGLNVEITREPVGVIGVISPWNFPIAIPAWKIAPALAFGNTVVLKSADLVPASAWALA 185 Query: 189 EIISRAGFPAGVFNLVMGSGRVVGDVLVNSPKVDGISFTGSVGVGRQIAVSCVSRQAKVQ 248 EIISRAG PAG FNLVMGSG VGD +VNSP +D ++FTGS +G I R AKVQ Sbjct: 186 EIISRAGLPAGAFNLVMGSGSKVGDTIVNSPDIDAVTFTGSDAIGNGIRGKVAGRGAKVQ 245 Query: 249 LEMGGKNPQIILDDADLKQAVELSVQSAFYSTGQRCTASSRLIVTAGIHDQFVAAMAERM 308 LEMGGKNP ++LDDADL A+ +V AF+ TGQRCTASSRLIVT GIHD FVA + ER+ Sbjct: 246 LEMGGKNPLVVLDDADLDTAINAAVDGAFFGTGQRCTASSRLIVTEGIHDAFVAGVIERL 305 Query: 309 KSIKVGHALKSGTDIGPVVSQAQLDQDLKYIDIGQSEGARLVSGGGLVTCDTEGYYLAPT 368 + ++ GHAL S + IGPV SQAQL DL+YI IG+ EGA L GG L+ DT GYYL+P Sbjct: 306 QGLRTGHALDSKSQIGPVSSQAQLQTDLEYISIGKEEGAHLAYGGELLQRDTPGYYLSPA 365 Query: 369 LFADSEAAMRISREEIFGPVANVVRVADYEAALAMANDTEFGLSAGIATTSLKYANHFKR 428 LF +++ MR++REE+FGPVA V+R +YE AL +ANDT FGL++GI TTSL+ + FKR Sbjct: 366 LFTETDNDMRLNREEVFGPVATVIRAKNYEEALELANDTRFGLTSGICTTSLESSKDFKR 425 Query: 429 HSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEFYTVVKTSYIG 480 +S+AGMVMVNLPTAG+DYHVPFGGRK SSYGSREQG YA+EF+T+VKT YIG Sbjct: 426 NSEAGMVMVNLPTAGIDYHVPFGGRKNSSYGSREQGSYAREFFTIVKTCYIG 477 Lambda K H 0.318 0.134 0.390 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: 676 Number of extensions: 20 Number of successful extensions: 1 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: 481 Length of database: 477 Length adjustment: 34 Effective length of query: 447 Effective length of database: 443 Effective search space: 198021 Effective search space used: 198021 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: 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