Alignments for a candidate for padB in Magnetospirillum magneticum AMB-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for padB in Magnetospirillum magneticum AMB-1

Align Phenylacetyl-CoA:acceptor oxidoreductase large subunit PadB; EC 1.8.5.3 (characterized, see rationale)
to candidate WP_011383653.1 AMB_RS06300 phenylacetyl CoA

Query= uniprot:A0A2R4BLL6
         (914 letters)



>NCBI__GCF_000009985.1:WP_011383653.1
          Length = 922

 Score = 1214 bits (3142), Expect = 0.0
 Identities = 567/902 (62%), Positives = 703/902 (77%), Gaps = 4/902 (0%)

Query: 10  VTKVATYCYQCVAGPDLLKVKVEDGVATAIEPNFDAEGVHPAAGRVCVKAFGLVQKTYNP 69
           V KV TYCYQCVAGPDL+ VKV DGVAT IEPNF A   HPA G+VCVKAFGL+QK+Y P
Sbjct: 13  VEKVQTYCYQCVAGPDLMTVKVVDGVATEIEPNFKAADTHPAEGKVCVKAFGLIQKSYTP 72

Query: 70  NRVLTPMKRTNPKKGRDEDPGFVPISWDEALDLIADKLNTVRANGLLDASGYPRVAASFG 129
           +R+LTPMKRTNPKKG+D+DPGFVPISWDEA+  IA++LN +RA GLLDA GYP+ AASFG
Sbjct: 73  HRILTPMKRTNPKKGKDQDPGFVPISWDEAMGTIAERLNAIRAEGLLDAQGYPKFAASFG 132

Query: 130 GGGTPTAYMGTFPAFLSAWGPVDLSFGSGQGVKCTHSEHLYGELWHRAFTVCPDTPRTKY 189
           G GTPT YMG+  AFLSAWGP+D  FGSGQGVKC HSEHLYGE WHR + + PDTPR  Y
Sbjct: 133 GAGTPTQYMGSLTAFLSAWGPIDFGFGSGQGVKCYHSEHLYGEFWHRGYVITPDTPRANY 192

Query: 190 IVSFGSNIEASGGVCGVWRHAEARVEQGVKRVQVEPHLSVTGGCSAEWVPIKPKTDPAFM 249
           I+S G+N EAS GVCGV+RHAEAR  +G  RVQVEPHLSVTG CSAEW+PIKPKTD AF+
Sbjct: 193 IISCGTNTEASSGVCGVYRHAEARA-RGAIRVQVEPHLSVTGACSAEWLPIKPKTDAAFL 251

Query: 250 HAMIHVMLFENARTRLDIDFLKHMTASPYLVAPNGLYLRDPDTRKPLVWDLKRAAAVPFD 309
             +++V++FE  R RLD+DFL++ T+SPYLV P+G YLRDP+T KPL+WD K   AVP D
Sbjct: 252 MTLLNVLVFEAPRERLDLDFLRNTTSSPYLVGPDGWYLRDPETHKPLLWDEKTGRAVPHD 311

Query: 310 TADIDPALDGEFTASGLEVL-PDNETVDHVQVRVLTAFGKLAEHERTFTPEWAAKVCDVP 368
           T    PAL+G FT      L  D +  +H  V  +TAF K  EH + +TP W AKVCDVP
Sbjct: 312 TPGAVPALEGRFTVPKAVTLGADEDRWEHTDVEGVTAFTKFIEHVKGYTPAWGAKVCDVP 371

Query: 369 ADTIRRVANEYLDHAQIGATIEIEGRTLPFRPVAITLGKTVNNGWGGYDCCWARTLMACL 428
              IR++AN++LDHA +G TIEI+G+ +P+RPVA+ LGKTVNNGWGG +CCWART++A L
Sbjct: 372 EARIRKIANDFLDHACVGQTIEIDGQVMPYRPVAVVLGKTVNNGWGGAECCWARTMLAVL 431

Query: 429 VGALDVPGGTIGTTVRLNRPASDRQSSAKPGPDGFMDYPFNPTDKENWVSRPQIRNANRT 488
           VGAL+VPGGT+GTT+R+NRPA++R  S +   DGFM+YPFNPTDK+ W + P IRNA + 
Sbjct: 432 VGALEVPGGTVGTTIRINRPAANRLESFEGCLDGFMEYPFNPTDKDTWKANPIIRNAYKM 491

Query: 489 LVPLVANSAWSAALGPTHLAWMQQRHGFENFPEPTQPDVWFFYRTNPVISFWDTPQVAEA 548
           LVPLV NS+WS ALGPT  ++M      +  P  T P+    YRTNPVISFWDT +VA  
Sbjct: 492 LVPLVGNSSWSPALGPTQFSYMFLDEPQDQIPRATFPEFLLVYRTNPVISFWDTDRVASV 551

Query: 549 VSKFPFVVAFTYTRDETNHFADVLLPDCTDLEGLQLIRIGGTKYVEQFWDKQGFALRQPA 608
           VS+ PFVV F +TRDETNHFAD+LLPD TDLEG+QLIRIGGTK+ EQFW +QGFALRQP+
Sbjct: 552 VSRMPFVVCFAHTRDETNHFADILLPDATDLEGMQLIRIGGTKFQEQFWKQQGFALRQPS 611

Query: 609 VVPQGETRDFTWIASELARRAGIQEPYNKAINRGAAGVPLKGASYDFSLDLEQTHGVEEI 668
           V PQGE RDFT IA++LA R G+QE Y  AINRG+ GVPLKG ++DFSL +++   +EE+
Sbjct: 612 VKPQGEARDFTDIATDLAVRTGLQEKYVAAINRGSHGVPLKGPNWDFSLPVDKAPSLEEV 671

Query: 669 WNASCRAASAELTGGAEDHGLDWWREHGFRTIDYPRLQWYLYPHMKDNGLRFEMPYQERI 728
           W+ASCR+ASAEL+ GAE  GLDWW+E+GFRTI +    W+L P +K  GLR+E+PYQER+
Sbjct: 672 WDASCRSASAELSDGAESQGLDWWKENGFRTIPFSETNWFLTPALKAKGLRYELPYQERL 731

Query: 729 FRIGTELGRRLHESGIDWWDRQLTEYQPLPDFHDFSHLIKSAVISNLGGREEDFPFWLLT 788
            RIG +L  RL E+GI WWD QLTEY+PL ++HDF    + +V+ + GG+  DFPFW++T
Sbjct: 732 TRIGRQLANRLKEAGITWWDHQLTEYRPLMEWHDFPGYWEQSVVEH-GGKVADFPFWVVT 790

Query: 789 SRSMQYAWGGNVSLQMVREVAANVAGHRGVIMNPASAAKLGIEDGDLVEVRSPL-RETRG 847
           +RSMQYAWG N+ + ++REV+ ++ GH GV+MNP +A K+G+++G+ + V +P  +   G
Sbjct: 791 ARSMQYAWGSNMHIPLMREVSGHIKGHDGVVMNPEAARKVGVKEGERIVVTAPTGKSVAG 850

Query: 848 RVVLRQGIRPDTLLMVGQFDHWITPYAKDFDVPSMNSLVPMLMDLTDATGSAADIVPVSI 907
           RVVL QGIRPDT+LM+ QFDHW TP AKDFDVPSMN L  M M LTDATGSAAD+  V+I
Sbjct: 851 RVVLSQGIRPDTILMMSQFDHWATPIAKDFDVPSMNRLTAMTMQLTDATGSAADLSRVAI 910

Query: 908 KR 909
           ++
Sbjct: 911 RK 912


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: 2798
Number of extensions: 121
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: 914
Length of database: 922
Length adjustment: 43
Effective length of query: 871
Effective length of database: 879
Effective search space:   765609
Effective search space used:   765609
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 17 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