GapMind for catabolism of small carbon sources

 

Aligments for a candidate for tdcE in Azospirillum brasilense Sp245

Align formate C-acetyltransferase (EC 2.3.1.54) (characterized)
to candidate AZOBR_RS30195 AZOBR_RS30195 formate acetyltransferase

Query= BRENDA::P09373
         (760 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS30195 AZOBR_RS30195 formate
           acetyltransferase
          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 Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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