Align 2-methylpropanoate--CoA ligase CCL4; HlCCL4; 2-methylbutanoate--CoA ligase CCL4; Butanoate--CoA ligase CCL3; Propionate--CoA ligase CCL3; EC 6.2.1.-; EC 6.2.1.17 (characterized)
to candidate 7025315 Shewana3_2475 AMP-binding domain protein (RefSeq)
Query= SwissProt::M4IQQ5 (556 letters) >FitnessBrowser__ANA3:7025315 Length = 574 Score = 163 bits (412), Expect = 2e-44 Identities = 156/565 (27%), Positives = 254/565 (44%), Gaps = 81/565 (14%) Query: 19 FLERAATVYGDCTSVVYDAVSYTWSQTHRRCLC----LASSIASLGIENGHVVSVLAPNV 74 +L A VY + +VV + W+ +R+ L LA+ + LGI G V + +PN Sbjct: 37 YLNDIANVYPEQLAVVVNHQDIRWN--YRQYLAQIDALATGLLKLGIGPGDRVGIWSPNN 94 Query: 75 PQMYELHFAVPMAGAILNAVNLRLDARTISILLHH-------------SESKLIFVDHLS 121 + FA GAI+ +N + L + S + L + L+ Sbjct: 95 IEWCLTQFATAKIGAIMVCINPAYRPEELQYALTNVGCRAVICADKFKSSNYLQMLYELA 154 Query: 122 RDLILEAIALFPKQAPVPRLVFMADESESGNSSELGKEFFCSYKDLIDRGDPDFKWVMPK 181 +L + A +A +P L F+ + L ++ DL+ D K + + Sbjct: 155 PELKVCAAGQLQAKA-LPDLQFVIRMGAEQSPGML------NFDDLLVEVTADDKAALER 207 Query: 182 -----SEWDPMILNYTSGTTSSPKGVVHCHRGIF---IMTVDSLIDWGVPKQPVYLWTLP 233 S +D + + +TSGTT SPKG H I + +++ K + +P Sbjct: 208 IAESLSPYDAINIQFTSGTTGSPKGATLSHHNILNNGYLVAEAMKFTCEDKLCI---PVP 264 Query: 234 MFHANGWSYPWGMAAVGGTNICLRK----------FDSEIIYDMIKRHGVTHMCGAPVVL 283 ++H G V G +CL K FD ++++R T + G P + Sbjct: 265 LYHCFGM--------VLGNLVCLAKGAAAVFPGDSFDPLTTLEVVERERCTALHGVPTMF 316 Query: 284 NMLSNAPGSE-----PLKTTVQIMTAGAPPPSAVLFRTESLGFA--VSHGYGLTETAGLV 336 P + L+T V AGA P V+ R ++L + V GYG TE + L Sbjct: 317 IAELEHPEFKRFDLSSLRTGVM---AGATCPEEVMRRVQNLMYMQEVLIGYGQTECSPL- 372 Query: 337 VSCAWKKEWNHLPATERARLKSRQGVGTVM-QTKIDVVDPVTGAAVKRDGSTLGEVVLRG 395 NH+ + K VG + T++ +VD G + + T GEV RG Sbjct: 373 ---------NHITEIDSPVEKRVLTVGRALPHTEVKIVDEF-GEVLPIN--TPGEVCSRG 420 Query: 396 GSVMLGYLKDPEGTAKSMTADGWFYTGDVGVMHPDGYLEIKDRSKDVIISGGENLSSVEV 455 +M Y DPE TA ++ ++GW ++GD+G M GY++I R KD+II GGEN+ E+ Sbjct: 421 YCIMQCYWNDPEKTAATIDSEGWLHSGDIGQMDEQGYVQIVGRIKDMIIRGGENIYPREI 480 Query: 456 ESILYSHPDILEAAVVARPDEFWGETPCAFVSLKKGLTKKPTEKEIVEYCRSKLPRYMVP 515 E LY+H D+ +AAV + +GE CA++ ++ G T +E++I + K + VP Sbjct: 481 EEKLYTHKDVQDAAVFGVHSDKYGEEVCAWIKIRSGAT--ISEEDIRHFLTEKFAYFKVP 538 Query: 516 KTVVFKEELPKTSTGKVQKFILRDM 540 + + F E+ P T TGK+QKF +R++ Sbjct: 539 RYIKFVEQYPMTVTGKIQKFKMREL 563 Lambda K H 0.319 0.135 0.412 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: 725 Number of extensions: 36 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 556 Length of database: 574 Length adjustment: 36 Effective length of query: 520 Effective length of database: 538 Effective search space: 279760 Effective search space used: 279760 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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