Alignments for a candidate for padB in Thauera aminoaromatica S2

GapMind for catabolism of small carbon sources

Alignments for a candidate for padB in Thauera aminoaromatica S2

Align Phenylacetyl-CoA:acceptor oxidoreductase large subunit PadB; EC 1.8.5.3 (characterized, see rationale)
to candidate WP_004301606.1 C665_RS04875 molybdopterin oxidoreductase

Query= uniprot:A0A2R4BLL6
         (914 letters)



>NCBI__GCF_000310185.1:WP_004301606.1
          Length = 917

 Score = 1221 bits (3158), Expect = 0.0
 Identities = 580/906 (64%), Positives = 701/906 (77%), Gaps = 6/906 (0%)

Query: 12  KVATYCYQCVAGPDLLKVKVEDGVATAIEPNFDAEGVHPAAGRVCVKAFGLVQKTYNPNR 71
           K+ +YCY CVAGPD + VKV DGVAT IEPNF A  VHPA GRVCVKA GLVQKTYNP+R
Sbjct: 11  KIPSYCYNCVAGPDFMTVKVIDGVATEIEPNFAAADVHPARGRVCVKAHGLVQKTYNPHR 70

Query: 72  VLTPMKRTNPKKGRDEDPGFVPISWDEALDLIADKLNTVRANGLLDASGYPRVAASFGGG 131
           +L PMKRTNPKKGR+EDPGFVPISWDEALD IA +L  VR  GL+D SG PRVAASFG G
Sbjct: 71  ILQPMKRTNPKKGRNEDPGFVPISWDEALDTIAARLAAVREKGLVDDSGLPRVAASFGHG 130

Query: 132 GTPTAYMGTFPAFLSAWGPVDLSFGSGQGVKCTHSEHLYGELWHRAFTVCPDTPRTKYIV 191
           GTP  YMGT PAFL+AWGP+D SFGSGQGVKC HSEHLYGE WHRAFTV  DTP  +Y++
Sbjct: 131 GTPAMYMGTLPAFLAAWGPIDFSFGSGQGVKCVHSEHLYGEFWHRAFTVAADTPNCRYVI 190

Query: 192 SFGSNIEASGGVCGVWRHAEARVEQGVKRVQVEPHLSVTGGCSAEWVPIKPKTDPAFMHA 251
           S GSN++ASGG C V RHA+ARV +G KRVQVEPHLS+TG C++EWVPI+PKTDPAFM A
Sbjct: 191 SIGSNVDASGGPCAVTRHADARV-RGYKRVQVEPHLSITGACASEWVPIRPKTDPAFMFA 249

Query: 252 MIHVMLFENARTRLDIDFLKHMTASPYLVAPNGLYLRDPDTRKPLVWDLKRAAAVPFDTA 311
           +IHV++ E+   +LD+ FL+  T+SPYLV P+GLYLR PD+ KPLVWD     AVPFDT 
Sbjct: 250 LIHVLVCEHGLGQLDLPFLRDRTSSPYLVGPDGLYLRAPDSAKPLVWDPAAGRAVPFDTP 309

Query: 312 DIDPALDGEF-TASGLEVLPDNETVDHVQVRVLTAFGKLAEHERTFTPEWAAKVCDVPAD 370
            ++PAL+G F  A+ + V  D+       V    A   L EH R +TPEWA  +CDVPA 
Sbjct: 310 GVEPALEGRFRVAAAVTVDADDARHALADVEGAPAHTMLVEHMRKYTPEWAEGICDVPAA 369

Query: 371 TIRRVANEYLDHAQIGATIEIEGRTLPFRPVAITLGKTVNNGWGGYDCCWARTLMACLVG 430
           TIRR+A EYL++AQ+GATIE++G TLP RPVA+TLGK+VNNGWG ++CCWART++A LVG
Sbjct: 370 TIRRIAGEYLENAQVGATIEVDGATLPLRPVAVTLGKSVNNGWGAFECCWARTVLATLVG 429

Query: 431 ALDVPGGTIGTTVRLNRPASDRQSSAKPGPDGFMDYPFNPTDKENWVSRPQIRNANRTLV 490
           AL+VPGGT+GTTVRLNRP  DR  S   G DGFM   FNPTDKE+WV+RP  RNA+RTLV
Sbjct: 430 ALEVPGGTLGTTVRLNRPHDDRHLSVAAGEDGFMAQKFNPTDKEHWVARPTGRNAHRTLV 489

Query: 491 PLVANSAWSAALGPTHLAWMQQRHGFENF--PEPTQPDVWFFYRTNPVISFWDTPQVAEA 548
           P+V NSAWS ALGPT LAWM QR    +F  P+PT PD+WF YR+NP ISFWDTP + E 
Sbjct: 490 PIVGNSAWSQALGPTQLAWMFQREVPRDFNMPKPTLPDIWFIYRSNPAISFWDTPSLVET 549

Query: 549 VSKFPFVVAFTYTRDETNHFADVLLPDCTDLEGLQLIRIGGTKYVEQFWDKQGFALRQPA 608
           ++ FPF V+F YT DETN FAD+LLP+ TDLE LQ+I++GGTK+VEQFW  +G  LRQPA
Sbjct: 550 IATFPFTVSFAYTVDETNFFADLLLPEATDLESLQMIKVGGTKFVEQFWTARGVVLRQPA 609

Query: 609 VVPQGETRDFTWIASELARRAGIQEPYNKAINRGAAGV-PLKGASYDFSLDLEQTHGVEE 667
           V PQGE RDFTWI++ELARR G+ EPYNKAINRGA GV PL G  YDFSLD  +TH V+ 
Sbjct: 610 VEPQGEARDFTWISTELARRTGLLEPYNKAINRGAGGVSPLAGEGYDFSLDPTRTHDVDT 669

Query: 668 IWNASCRAASAELTGGAEDHGLDWWREHGFRTIDYPRLQWYLYPHMKDNGLRFEMPYQER 727
           IW+A CRAAS +L+ G E H L W++EHGF T+  P+  WYL P + + GLR+E+PYQER
Sbjct: 670 IWDAICRAASTDLSQGQETHDLAWFKEHGFYTVPMPQRSWYLTPTLAEKGLRYELPYQER 729

Query: 728 IFRIGTELGRRLHESGIDWWDRQLTEYQPLPDFHDFSHLIKSAVISNLGGREEDFPFWLL 787
           + RIG ELG RLHE  + WWD QL+EY  LP++HD     + A++ + G + ED+P WLL
Sbjct: 730 LLRIGRELGNRLHEHDMHWWDTQLSEYTALPEWHDVPGRWEQALVDS-GAKPEDYPLWLL 788

Query: 788 TSRSMQYAWGGNVSLQMVREVAANVAGHRGVIMNPASAAKLGIEDGDLVEVRSPLRETRG 847
            ++SMQY  GGNVS+ ++REVA NV GH GVIMN  +A +LGI DGD VE+RS +  T G
Sbjct: 789 ATKSMQYHTGGNVSIALMREVAQNVRGHAGVIMNANTARRLGIADGDRVEIRSHIGATYG 848

Query: 848 RVVLRQGIRPDTLLMVGQFDHWITPYAKDFDVPSMNSLVPMLMDLTDATGSAADIVPVSI 907
           + VL  GIRPDTL++ GQFDHW TP AKDF +PS+N++ PM ++LTDATGS ADIV V+I
Sbjct: 849 KAVLAHGIRPDTLVIPGQFDHWATPVAKDFGMPSLNTVAPMSLELTDATGSGADIVRVAI 908

Query: 908 KRVGGA 913
           +R+ G+
Sbjct: 909 RRLEGS 914


Lambda     K      H
   0.320    0.137    0.438 

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: 2823
Number of extensions: 119
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: 914
Length of database: 917
Length adjustment: 43
Effective length of query: 871
Effective length of database: 874
Effective search space:   761254
Effective search space used:   761254
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 (21.8 bits)
S2: 57 (26.6 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources