Align phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate GFF1302 Psest_1335 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II
Query= BRENDA::A7KUK6 (562 letters) >FitnessBrowser__psRCH2:GFF1302 Length = 563 Score = 218 bits (555), Expect = 5e-61 Identities = 164/526 (31%), Positives = 249/526 (47%), Gaps = 43/526 (8%) Query: 46 TYKSLRDASLDFGKGLKALYEWRKGDVLALFTPNSIDTPVVMWGTLWAGGTISPANPGYT 105 TY L S DF L+ + + GD +A+ PN I P+V++G + AG + NP YT Sbjct: 51 TYGELYKLSGDFAAYLQQNTDLQPGDRIAVQLPNLIQYPIVVFGAMRAGLIVVNTNPLYT 110 Query: 106 VDELAFQLKNSHAKGLVTQASVLPVAREAAKKVGMPEDRIILIGDQRDPDARVKHFTSVR 165 E+ Q ++ AK LV A++ +A E K G+ I + D P R+ V+ Sbjct: 111 AREMEHQFNDAGAKALVCLANMAHLAEEVLPKTGIKHVVITEVADMLPPLKRMLVNAVVK 170 Query: 166 NIS--------------------GATRYRKQKITPAKDVAFLVYSSGTTGVPKGVMISHR 205 ++ G + ++ + + DVA L Y+ GTTGV KG M++HR Sbjct: 171 HVKKMVPAYSLPKAVKLNDALALGRGKPVREALPKSDDVAVLQYTGGTTGVAKGAMLTHR 230 Query: 206 NIVANIRQQFIAEGEMLSWNGGPDGKGDRVLAFLPFYHIYGLTCLITQALYKGYHLIVMS 265 NIVAN+ Q G L+ DG + ++A LP YHIY T + G H I++S Sbjct: 231 NIVANMLQCKALMGSNLN-----DGS-EVLIAPLPLYHIYAFTFHCMAMMLSGNHNILIS 284 Query: 266 K-FDIEKWCAHVQNYRCSFSYIVPPVVLLLGKHPVVDKYDLSSLRMMNSGAAPLTQELVE 324 D+ + YR S + + + L K D S+L++ SG L E Sbjct: 285 NPRDLPAMIKDLGKYRFSGFVGLNTLFVALCNSEDFRKLDFSALKVTLSGGMALQLATAE 344 Query: 325 AVYSRIKVGIKQGYGLSETSPTTHSQRWEDWREAMGSVGRLMPNMQAKYMTMPEDGSEPK 384 I +GYGL+ETSP E + +GS+G +P+ Q K + +DG + Sbjct: 345 RWKQVTGCPICEGYGLTETSPVASVNPIEHIQ--LGSIGIPVPSTQFKVIN--DDG---Q 397 Query: 385 EVGEGEVGELYLKGPNVFLGYHENPEATKGCLSEDGWFQTGDVGYQDAKGNFYITDRVKE 444 ++ +GE+GEL +KGP V GY + PEAT + GWF+TGD+G G I DR K+ Sbjct: 398 DLAQGEIGELCIKGPQVMKGYWQRPEATDEVIDAQGWFKTGDIGVIQEDGYIRIVDRKKD 457 Query: 445 LIKYKGFQVPPAELEGYLVDNDAIDDVAVIGIESETHGSEVPMACVVRSAKSKSSGTSEK 504 +I GF V P ELE L + A IG+ E G + + VV+ +S + Sbjct: 458 MILVSGFNVYPNELEDVLASLPGVLQSAAIGVPDEKSGEAIKLFVVVKPGESLTK----- 512 Query: 505 DEAARIIKWLDSKVASHKRLRGGVHFVDEIPKNPSGKILRRILKQK 550 ++++ + + +KR + V F D +P GKILRR L+ + Sbjct: 513 ---EQVMQHMHDNLTGYKRPK-AVEFRDSLPTTNVGKILRRELRDE 554 Lambda K H 0.317 0.136 0.410 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: 669 Number of extensions: 30 Number of successful extensions: 6 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: 562 Length of database: 563 Length adjustment: 36 Effective length of query: 526 Effective length of database: 527 Effective search space: 277202 Effective search space used: 277202 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: 53 (25.0 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