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_011384418.1 AMB_RS10170 phenylacetyl CoA

Query= uniprot:A0A2R4BLL6
         (914 letters)



>NCBI__GCF_000009985.1:WP_011384418.1
          Length = 911

 Score = 1147 bits (2967), Expect = 0.0
 Identities = 546/901 (60%), Positives = 666/901 (73%), Gaps = 3/901 (0%)

Query: 13  VATYCYQCVAGPDLLKVKVEDGVATAIEPNFDAEGVHPAAGRVCVKAFGLVQKTYNPNRV 72
           V TYCY CVAGPDL+ V V+DGVA A+ PN    G+HPA GR CVKA+GLVQKTYNP+RV
Sbjct: 8   VPTYCYNCVAGPDLMCVTVKDGVAVAVTPNHAGMGIHPADGRPCVKAYGLVQKTYNPHRV 67

Query: 73  LTPMKRTNPKKGRDEDPGFVPISWDEALDLIADKLNTVRANGLLDASGYPRVAASFGGGG 132
           LTPMKRTNP+KGRDEDPGFVPISWDEALDL+A KL +VR  GLL+  G PR+AA+FG GG
Sbjct: 68  LTPMKRTNPRKGRDEDPGFVPISWDEALDLVAGKLRSVREMGLLNEQGMPRLAATFGHGG 127

Query: 133 TPTAYMGTFPAFLSAWGPVDLSFGSGQGVKCTHSEHLYGELWHRAFTVCPDTPRTKYIVS 192
           TP  YMGTFPAFL+AWGP+D SFGSGQGVKC HSEHLYGE WHRAFTV  DTP   +IVS
Sbjct: 128 TPANYMGTFPAFLAAWGPIDFSFGSGQGVKCVHSEHLYGEYWHRAFTVAADTPNANFIVS 187

Query: 193 FGSNIEASGGVCGVWRHAEARVEQGVKRVQVEPHLSVTGGCSAEWVPIKPKTDPAFMHAM 252
           FG+N+E SGG CGV RHA+AR+ +G+KRVQVEPHLS TG CSA+WVPI+PKTDPAFM AM
Sbjct: 188 FGTNVEVSGGPCGVRRHADARI-RGIKRVQVEPHLSPTGACSAQWVPIRPKTDPAFMFAM 246

Query: 253 IHVMLFENARTRLDIDFLKHMTASPYLVAPNGLYLRDPDTRKPLVWDLKRAAAVPFDTAD 312
           +HVML E  R+ LD+DFL+  TASPYLV   G YLRD  T KPL+WD      VP D   
Sbjct: 247 LHVMLHEAPRSALDLDFLRDRTASPYLVDDEGWYLRDEATGKPLMWDGITGQPVPHDHPG 306

Query: 313 IDPALDGEFTA-SGLEVLPDNETVDHVQVRVLTAFGKLAEHERTFTPEWAAKVCDVPADT 371
             PAL+G FT  + +  LPD E V        TAF  L +  R +TP+WA  +CDVPA  
Sbjct: 307 AVPALEGSFTVPAAVAKLPDGEMVRRENATARTAFTLLVDGMRGYTPDWAETICDVPAKV 366

Query: 372 IRRVANEYLDHAQIGATIEIEGRTLPFRPVAITLGKTVNNGWGGYDCCWARTLMACLVGA 431
           +R+VA EYLD+A +G T E++G+ LP RPVA+TLGKTVNNGWG Y+CCWART++A LVGA
Sbjct: 367 VRQVALEYLDNACVGQTTEVDGKVLPHRPVAVTLGKTVNNGWGAYECCWARTVLATLVGA 426

Query: 432 LDVPGGTIGTTVRLNRPASDRQSSAKPGPDGFMDYPFNPTDKENWVSRPQIRNANRTLVP 491
           L+VPGGT+GTTVRLNRP  +R  S KPG DGFM+   N T K  W  +P+ RNA+ TL+P
Sbjct: 427 LEVPGGTLGTTVRLNRPYENRLKSVKPGEDGFMNAQMNSTKKGGWAEKPKGRNAHTTLIP 486

Query: 492 LVANSAWSAALGPTHLAWMQQRHGFENFPEPTQPDVWFFYRTNPVISFWDTPQVAEAVSK 551
           +V +S+W+ ALGPTHLAWM  +     +  P  PDVW  YRTNP ISFWDT Q++  ++K
Sbjct: 487 IVGDSSWAQALGPTHLAWMFLKDSPAEWAPPEPPDVWIAYRTNPAISFWDTAQLSGNMAK 546

Query: 552 FPFVVAFTYTRDETNHFADVLLPDCTDLEGLQLIRIGGTKYVEQFWDKQGFALRQPAVVP 611
            PFVV F YT DETNH AD+LLP+ TDLE  QLIR GG+K+VEQ W  QGF LRQPAV P
Sbjct: 547 MPFVVCFAYTMDETNHMADILLPEATDLESTQLIRAGGSKFVEQHWQHQGFVLRQPAVAP 606

Query: 612 QGETRDFTWIASELARRAGIQEPYNKAINRGAAGVPLKGASYDFSLDLEQTHGVEEIWNA 671
           QGE+RDFTWI +EL+RR G+ E YN+ +N+G A VPLKG  +DF+L  +Q H V+ IW+A
Sbjct: 607 QGESRDFTWITTELSRRVGLLESYNRGLNKGFALVPLKGEGFDFTLPEDQVHDVDTIWDA 666

Query: 672 SCRAASAELTGGAEDHGLDWWREHGFRTIDYPRLQWYLYPHMKDNGLRFEMPYQERIFRI 731
            C+AA+A  T G E  GLDW +E+GF    + R  WYL+  M + GLR+E+PYQER+ R+
Sbjct: 667 VCKAATAGATKGQEVRGLDWMKENGFFMQPFAREDWYLHATMVEQGLRYELPYQERLMRV 726

Query: 732 GTELGRRLHESGIDWWDRQLTEYQPLPDFHDFSHLIKSAVISNLGGREEDFPFWLLTSRS 791
           G EL RRLHE+GI WWD QL EYQ +P +HD       AV    G + EDFPFW +T+++
Sbjct: 727 GEELRRRLHEAGIQWWDEQLEEYQGIPHWHDVPGRWVKAV-ERAGAKAEDFPFWGITTKT 785

Query: 792 MQYAWGGNVSLQMVREVAANVAGHRGVIMNPASAAKLGIEDGDLVEVRSPLRETRGRVVL 851
           M Y  G N  + ++ EVA N+ GH  VI+N +SAAKL I+DGD VEV S +  TRGR  L
Sbjct: 786 MPYTTGNNAGIPLMNEVAGNLRGHGSVIINASSAAKLDIKDGDWVEVSSVVGHTRGRAAL 845

Query: 852 RQGIRPDTLLMVGQFDHWITPYAKDFDVPSMNSLVPMLMDLTDATGSAADIVPVSIKRVG 911
            QG RPDT+++ GQF HW TPYAKD + PS+N++  M ++LTDATGS AD+V V+++RV 
Sbjct: 846 VQGCRPDTVVIPGQFQHWKTPYAKDLNFPSLNTITQMSLELTDATGSGADVVRVALRRVD 905

Query: 912 G 912
           G
Sbjct: 906 G 906


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: 2759
Number of extensions: 127
Number of successful extensions: 4
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: 911
Length adjustment: 43
Effective length of query: 871
Effective length of database: 868
Effective search space:   756028
Effective search space used:   756028
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: 56 (26.2 bits)

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

Links

Downloads

Related tools

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:

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