Align formate C-acetyltransferase (EC 2.3.1.54) (characterized)
to candidate AZOBR_RS30195 AZOBR_RS30195 formate acetyltransferase
Query= BRENDA::P09373 (760 letters) >FitnessBrowser__azobra:AZOBR_RS30195 Length = 760 Score = 973 bits (2514), Expect = 0.0 Identities = 486/746 (65%), Positives = 578/746 (77%), Gaps = 11/746 (1%) Query: 12 WEGFTKGDWQNEVNVRDFIQKNYTPYEGDESFLAGATEATTTLWDKVMEGVKLENRTHAP 71 W F G WQ EVNVRDFI +N PY GD FL G T T LWDKV +K E Sbjct: 21 WRRFVPGVWQQEVNVRDFIVRNVHPYAGDSRFLTGPTGRTKALWDKVTALLKEERAAKGG 80 Query: 72 V-DFDTAVASTITSHDAGYINKQLEKIVGLQTEAPLKRALIPFGGIKMIEGSCKAYNREL 130 V D DT V +IT+H GYI+++LE +VGLQT+ PLKRA++PFGG +M++ +AY + Sbjct: 81 VLDADTEVFGSITAHAPGYIDRELEIVVGLQTDKPLKRAIMPFGGWRMVKNGLEAYGFKP 140 Query: 131 DPMIKKIFTEYRKTHNQGVFDVYTPDILRCRKSGVLTGLPDAYGRGRIIGDYRRVALYGI 190 P ++++F RK+HN GVFDVYT ++LRCRKSGV+TGLPDAYGRGRIIGDYRR+ALYG Sbjct: 141 SPKLEEVFPGLRKSHNDGVFDVYTEEMLRCRKSGVITGLPDAYGRGRIIGDYRRLALYGA 200 Query: 191 DYLMKDKLAQFTSLQADLENGVNLEQTIRLREEIAEQHRALGQMKEMAAKYGYDISGPAT 250 +L++DK AQ+ SL+ D + E T+RLREEI EQ +AL ++ MA YG+D+S PA Sbjct: 201 TFLIEDKKAQYKSLEVDRID----EHTLRLREEITEQIKALKELAAMAKSYGFDVSRPAA 256 Query: 251 NAQEAIQWTYFGYLAAVKSQNGAAMSFGRTSTFLDVYIERDLKAGKITEQEAQEMVDHLV 310 +A+EA+QWTY YLAAVK NGAAMS GR S+FLDVY+ERDL+ G +TE+EAQE++D V Sbjct: 257 SAREAVQWTYLAYLAAVKEANGAAMSLGRVSSFLDVYVERDLRDGLLTEEEAQELIDQFV 316 Query: 311 MKLRMVRFLRTPEYDELFSGDPIWATESIGGMGLDGRTLVTKNSFRFLNTLYTMGPSPEP 370 KLR+VRFLRTPEYD+LFSGDP W TE IGGM LDGRTLVTKNSFR L TL +GP+PEP Sbjct: 317 TKLRIVRFLRTPEYDQLFSGDPTWVTECIGGMALDGRTLVTKNSFRMLQTLNNLGPAPEP 376 Query: 371 NMTILWSEKLPLNFKKFAAKVSIDTSSLQYENDDLMRPDFNNDDYAIACCVSPMIVGKQM 430 N+T+LWSE LP FKKF A+ SI T S+QYENDDLMRP F DDY IACCVS M +GKQM Sbjct: 377 NLTVLWSESLPEGFKKFCAETSIKTCSVQYENDDLMRP-FWGDDYGIACCVSAMRIGKQM 435 Query: 431 QFFGARANLAKTMLYAINGGVDEKLKMQVGPKSEPIKGDVLNYDEVMERMDHFMDWLAKQ 490 QFFGARANLAKT+LYAINGG DE QVGP PI G+VL++D V+ R+ M+WLA+ Sbjct: 436 QFFGARANLAKTLLYAINGGRDEVSGEQVGPAFAPITGEVLDHDTVVARLLPMMEWLARA 495 Query: 491 YITALNIIHYMHDKYSYEASLMALHDRDVIRTMACGIAGLSVAADSLSAIKYAKVKPIRD 550 Y+ LN IH+MHDKY YE MALHDRDV+RTMACGIAGLSV ADSLSAIK+A VK +RD Sbjct: 496 YMNTLNAIHFMHDKYMYERLEMALHDRDVLRTMACGIAGLSVVADSLSAIKHATVKVVRD 555 Query: 551 EDGLAIDFEIEGEYPQFGNNDPRVDDLAVDLVERFMKKIQKLHTYRDAIPTQSVLTITSN 610 E GLA DF IEG+YP FGNND RVD +AV LVE FM ++K YRDA+PTQSVLTITSN Sbjct: 556 ERGLATDFVIEGDYPAFGNNDDRVDGIAVWLVETFMGLLRKQKAYRDAVPTQSVLTITSN 615 Query: 611 VVYGKKTGNTPDGRRAGAPFGPGANPMHGRDQKGAVASLTSVAKLPFAYAKDGISYTFSI 670 VVYGKKTGNTPDGR+AG PF PGANPMHGRD+KGA+AS+ SVAKLP+A+A+DGISYTF+I Sbjct: 616 VVYGKKTGNTPDGRKAGQPFAPGANPMHGRDRKGAIASMASVAKLPYAHAQDGISYTFTI 675 Query: 671 VPNALGKDDEVRKTNLAGLMDGYFHHEASIEGGQHLNVNVMNREMLLDAMENPEKYPQLT 730 VP ALG + R NL G++DGYF +GG H+NVNV +RE LL AM++PE YPQLT Sbjct: 676 VPGALGPTEGERVANLVGMLDGYFG-----QGGHHINVNVFDRETLLHAMDHPELYPQLT 730 Query: 731 IRVSGYAVRFNSLTKEQQQDVITRTF 756 IRVSGYAV F LT+EQQ DVI+RTF Sbjct: 731 IRVSGYAVNFIKLTREQQMDVISRTF 756 Lambda K H 0.318 0.135 0.393 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: 1431 Number of extensions: 48 Number of successful extensions: 5 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: 760 Length of database: 760 Length adjustment: 40 Effective length of query: 720 Effective length of database: 720 Effective search space: 518400 Effective search space used: 518400 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: 55 (25.8 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