Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_231851071.1 SUTH_RS00430 acyl-CoA dehydrogenase family protein
Query= reanno::acidovorax_3H11:Ac3H11_2991 (396 letters) >NCBI__GCF_000828635.1:WP_231851071.1 Length = 392 Score = 263 bits (671), Expect = 8e-75 Identities = 151/391 (38%), Positives = 224/391 (57%), Gaps = 12/391 (3%) Query: 1 MSIPANLPGLNFQLGEDIDALRDAVRDFAQAEIAPRAADIDKSDQFPMDLWRKMGDLGVL 60 MSIP L ED +A RD VR F + E+AP A ++ D+W K G G+L Sbjct: 14 MSIPRTL------FEEDHEAFRDTVRRFMEQEVAPHHARWEEQSHVDRDIWNKAGAAGLL 67 Query: 61 GITVPEQYGGAAMGYLAHMVAMEEISRASASVGLSYGAHSNLCVNQINRNGNEAQKAKYL 120 T+PE+YGG + ++ MEE +R +A+ GL +G HS + + G+E K KYL Sbjct: 68 CATMPEEYGGVGVDKRFSVIVMEEAARINAT-GLGWGLHSEIVAPYLLHYGSEHLKQKYL 126 Query: 121 SKLISGEHVGALAMSEPGAGSDVISMKLKAEDKGGYYLLNGSKMWITNGPDADTLVVYAK 180 K+ SGE VGA+AM+EP AGSD+ ++ A G +Y++NGSK++ITNG D ++V AK Sbjct: 127 PKMASGEMVGAIAMTEPAAGSDLQGVRTTAVKDGDHYIVNGSKIFITNGYLCDLVIVVAK 186 Query: 181 TEPELGARGVTAFLIEKGMKGFSIAQKLDKLGMRGSHTGELVFQDVEVPAENVLGGLNQG 240 T+P GA+G + +++ M GF+ A+ L K GM+ T EL F +V VPAEN+LG G Sbjct: 187 TDPAKGAKGTSLLVVDTSMPGFTKAKPLHKAGMKAQDTCELFFDNVRVPAENLLGEEGNG 246 Query: 241 AKVLMSGLDYERAVLTGGPLGIMQSVMDNVIPYIHDRKQFGQSIGEFQLIQGKVADMYTV 300 LM L +ER + + ++ +D + Y +RK FGQ I +FQ + K+A++ T Sbjct: 247 FVYLMQELPWERLQIAVIAMASAEAAIDWTVAYTRERKAFGQEIMKFQNTRFKLAELKTE 306 Query: 301 LQAGRSFAYTVAKNLDMLGTDHVRQVRKDCASVILWCAEKATWMAGEGVQIYGGNGYINE 360 +Q GR F V + +++L + + A WC + + E VQ++GG GY+ E Sbjct: 307 VQIGRVF---VDRCVELLLNNKLDPATASMAK--YWCTDLQFKVMDECVQLHGGYGYMWE 361 Query: 361 YPLGRLWRDAKLYEIGAGTSEIRRMLIGREL 391 YP+ R W DA++ I GT+EI + LI R L Sbjct: 362 YPITRAWADARVQRIYGGTNEIMKELISRSL 392 Lambda K H 0.318 0.136 0.400 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: 380 Number of extensions: 13 Number of successful extensions: 3 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: 396 Length of database: 392 Length adjustment: 31 Effective length of query: 365 Effective length of database: 361 Effective search space: 131765 Effective search space used: 131765 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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