Align Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized)
to candidate WP_011384974.1 AMB_RS13050 aldehyde dehydrogenase family protein
Query= curated2:Q49Z69 (475 letters) >NCBI__GCF_000009985.1:WP_011384974.1 Length = 479 Score = 435 bits (1118), Expect = e-126 Identities = 227/467 (48%), Positives = 307/467 (65%), Gaps = 2/467 (0%) Query: 8 YINGEWVESTSGETL-EVINPATEEVAGTIAKGNKEDVEKAVEAADNVYLEFRHTSVKER 66 Y++G WV+ G L +VINPATE+V+G +A G +D +A++AA + + T + ER Sbjct: 8 YVDGAWVKPAKGSRLLDVINPATEQVSGRVALGGADDAVRAIQAAAKAFPAWAATPLAER 67 Query: 67 QDLLDQIVQEYKNRKEDLIQAITDELGAPLS-VAENVHYQMGLDHFEAARDALNDFQFEE 125 ++L ++ Y+ R +++ +AI+ E+GAPL +A+ + GL HF+ A + FE Sbjct: 68 LEILAKVTAGYERRLDEIAEAISLEMGAPLERLAKPAQARAGLGHFKTALSLAKTYAFER 127 Query: 126 RRGDDLVVKEAIGVSGLITPWNFPTNQTSLKLAAAFAAGSPVVFKPSEETPFAAIILAEI 185 R+G LVVKE +GV LITPWN+P NQ + K+A A AAG +V KPSE P++A ILAEI Sbjct: 128 RQGTTLVVKEPVGVVSLITPWNWPMNQIACKVAPALAAGCAMVLKPSEFAPYSARILAEI 187 Query: 186 FDKVGVPKGVFNLVNGDGQGVGNPLSEHPKVRMMSFTGSGPTGSSIMKKAAEDFKKVSLE 245 + GVP GVFN+V GDG +G LS HP V M+S TGS GSS+M++ A KKVSLE Sbjct: 188 IHEAGVPAGVFNMVFGDGAEIGPVLSSHPLVDMVSLTGSNLAGSSVMREGAATIKKVSLE 247 Query: 246 LGGKSPYIILDDADIDGAASAAANKVVFNTGQVCTAGTRTIVPASIKEDFLTAVKEKFSQ 305 LGGKS II D AD A A ++ NTGQ C A +R VPA ++ E +Q Sbjct: 248 LGGKSANIICDSADFKKAIGHAVKAMMGNTGQSCNAPSRLFVPAHRLDEAEGLAAELCAQ 307 Query: 306 VKVGNPREEGTQVGPIISKKQFDQVQAYIDKGIEEGAELLYGGPGKPEGLDKGYFARPTI 365 +KVG+P + T +GPI + +QFD+V+ I G+EEGA+L+ GGP +PEGLDKGYF RPT+ Sbjct: 308 IKVGDPSDPETVMGPIANGRQFDKVRRMIRTGMEEGAKLVCGGPERPEGLDKGYFVRPTV 367 Query: 366 FNNVDNSMTIAQEEIFGPVMSVITYNDLDEAIKIANDTKYGLAGYVYGSDKDTLHKVARS 425 F+ V ++MTI +EEIFGPV+S+ Y DLD+A+ AND YGL+GYVY D D VAR Sbjct: 368 FSRVTDAMTIMREEIFGPVLSMRGYADLDDAVAGANDCVYGLSGYVYAGDLDEARAVARR 427 Query: 426 IEAGTVEINEAGRKPDLPFGGYKQSGLGREWGDYGIEEFLEVKSIAG 472 + G V +N A P PFGG +QSG+GREWG+ G EEFLE K++ G Sbjct: 428 LRTGMVHLNGALSHPGGPFGGIRQSGVGREWGEAGFEEFLESKTLFG 474 Lambda K H 0.313 0.134 0.380 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: 614 Number of extensions: 29 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: 475 Length of database: 479 Length adjustment: 33 Effective length of query: 442 Effective length of database: 446 Effective search space: 197132 Effective search space used: 197132 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 51 (24.3 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