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_004303018.1 C665_RS06145 molybdopterin oxidoreductase

Query= uniprot:A0A2R4BLL6
         (914 letters)



>NCBI__GCF_000310185.1:WP_004303018.1
          Length = 913

 Score = 1705 bits (4415), Expect = 0.0
 Identities = 808/912 (88%), Positives = 851/912 (93%)

Query: 3   TPNCPTGVTKVATYCYQCVAGPDLLKVKVEDGVATAIEPNFDAEGVHPAAGRVCVKAFGL 62
           T + P G TKVATYCYQCVAGPDLLKVKVEDGVATA+EPNFDAE VHPAAGRVCVKAFGL
Sbjct: 2   TVSSPQGTTKVATYCYQCVAGPDLLKVKVEDGVATAVEPNFDAEDVHPAAGRVCVKAFGL 61

Query: 63  VQKTYNPNRVLTPMKRTNPKKGRDEDPGFVPISWDEALDLIADKLNTVRANGLLDASGYP 122
           VQKTYNPNRVL PMKRTNPKKGR EDP FVPISWDEALD IA KL  +R  GLLDASGYP
Sbjct: 62  VQKTYNPNRVLQPMKRTNPKKGRHEDPRFVPISWDEALDTIAAKLRGIRETGLLDASGYP 121

Query: 123 RVAASFGGGGTPTAYMGTFPAFLSAWGPVDLSFGSGQGVKCTHSEHLYGELWHRAFTVCP 182
           RVAASFGGGGTPTAYMGTFPA L+AWGPVD+SFGSGQGVKC HSEHLYGELWHRAF VCP
Sbjct: 122 RVAASFGGGGTPTAYMGTFPALLAAWGPVDMSFGSGQGVKCYHSEHLYGELWHRAFIVCP 181

Query: 183 DTPRTKYIVSFGSNIEASGGVCGVWRHAEARVEQGVKRVQVEPHLSVTGGCSAEWVPIKP 242
           DTPR+KYI+SFGSNIEASGGVCGVWRHA ARVEQGVKRVQVEPHLSVTGGCSAEW+PIKP
Sbjct: 182 DTPRSKYILSFGSNIEASGGVCGVWRHAAARVEQGVKRVQVEPHLSVTGGCSAEWLPIKP 241

Query: 243 KTDPAFMHAMIHVMLFENARTRLDIDFLKHMTASPYLVAPNGLYLRDPDTRKPLVWDLKR 302
           KTD A MHAMIHVMLFENAR+RLDIDFLKHMTASPYLVAPNG YLRDPDTRKPLVWDLK 
Sbjct: 242 KTDAACMHAMIHVMLFENARSRLDIDFLKHMTASPYLVAPNGFYLRDPDTRKPLVWDLKS 301

Query: 303 AAAVPFDTADIDPALDGEFTASGLEVLPDNETVDHVQVRVLTAFGKLAEHERTFTPEWAA 362
             AV FDT  IDPALDG+F ASGLEVLPD E V H    V +AFGKL +HERTFTPEWA 
Sbjct: 302 GKAVVFDTPGIDPALDGDFLASGLEVLPDQELVTHEAAPVRSAFGKLLDHERTFTPEWAQ 361

Query: 363 KVCDVPADTIRRVANEYLDHAQIGATIEIEGRTLPFRPVAITLGKTVNNGWGGYDCCWAR 422
            +CDVPA TIRR+ANEYLDHA+IGATIEIEGRTLP+RPVA+TLGKTVNNGWGGYDCCWAR
Sbjct: 362 GICDVPAATIRRIANEYLDHAEIGATIEIEGRTLPYRPVAVTLGKTVNNGWGGYDCCWAR 421

Query: 423 TLMACLVGALDVPGGTIGTTVRLNRPASDRQSSAKPGPDGFMDYPFNPTDKENWVSRPQI 482
           TLMACLVGALDVPGGTIGT VRLNRPA+DRQSSAKPG DGFMDYPFNPTDKENW+SRPQI
Sbjct: 422 TLMACLVGALDVPGGTIGTAVRLNRPANDRQSSAKPGVDGFMDYPFNPTDKENWISRPQI 481

Query: 483 RNANRTLVPLVANSAWSAALGPTHLAWMQQRHGFENFPEPTQPDVWFFYRTNPVISFWDT 542
           RNANRTLVPLVANSAWSAALGPTHLAWMQQRHGFE+FPEPTQPDVWFFYRTNPVISFWDT
Sbjct: 482 RNANRTLVPLVANSAWSAALGPTHLAWMQQRHGFESFPEPTQPDVWFFYRTNPVISFWDT 541

Query: 543 PQVAEAVSKFPFVVAFTYTRDETNHFADVLLPDCTDLEGLQLIRIGGTKYVEQFWDKQGF 602
           PQVAEAV+KFPFVVAFTYTRDETNHFAD+LLPDCTDLEGLQ++RIGGTKYVEQFWD QGF
Sbjct: 542 PQVAEAVAKFPFVVAFTYTRDETNHFADILLPDCTDLEGLQMLRIGGTKYVEQFWDHQGF 601

Query: 603 ALRQPAVVPQGETRDFTWIASELARRAGIQEPYNKAINRGAAGVPLKGASYDFSLDLEQT 662
           ALRQP V  QG+TRDFTWI++ELARRAGI EPYNKAINRGAAGVPLKG +YDFSL  +  
Sbjct: 602 ALRQPVVPTQGDTRDFTWISTELARRAGILEPYNKAINRGAAGVPLKGPNYDFSLQPDHA 661

Query: 663 HGVEEIWNASCRAASAELTGGAEDHGLDWWREHGFRTIDYPRLQWYLYPHMKDNGLRFEM 722
           +GVEEIW+ASCRAASAELT GAEDHGL+WW+EHGFRTI YPRLQWYLYPH+ D GLRFEM
Sbjct: 662 YGVEEIWDASCRAASAELTEGAEDHGLEWWKEHGFRTIKYPRLQWYLYPHLVDQGLRFEM 721

Query: 723 PYQERIFRIGTELGRRLHESGIDWWDRQLTEYQPLPDFHDFSHLIKSAVISNLGGREEDF 782
           PYQERI+RIG ELGRRLHESGIDWWDRQLTEY+PLP+FHDFSHLIK AVISNLGGR+EDF
Sbjct: 722 PYQERIYRIGEELGRRLHESGIDWWDRQLTEYRPLPEFHDFSHLIKHAVISNLGGRDEDF 781

Query: 783 PFWLLTSRSMQYAWGGNVSLQMVREVAANVAGHRGVIMNPASAAKLGIEDGDLVEVRSPL 842
           PFWLLT+RSMQY+WGGNVSLQMVREVAANV GHRGVIMNP +A KLGIEDGDLVEVRSPL
Sbjct: 782 PFWLLTARSMQYSWGGNVSLQMVREVAANVKGHRGVIMNPTAARKLGIEDGDLVEVRSPL 841

Query: 843 RETRGRVVLRQGIRPDTLLMVGQFDHWITPYAKDFDVPSMNSLVPMLMDLTDATGSAADI 902
           RETRGRVVLRQGIRPDTLLMVGQFDHWITPYAKDFDVPSMN+LVPMLMDLTDATGSAADI
Sbjct: 842 RETRGRVVLRQGIRPDTLLMVGQFDHWITPYAKDFDVPSMNALVPMLMDLTDATGSAADI 901

Query: 903 VPVSIKRVGGAQ 914
           VPVSIKR+GGAQ
Sbjct: 902 VPVSIKRIGGAQ 913


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: 3189
Number of extensions: 113
Number of successful extensions: 1
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: 913
Length adjustment: 43
Effective length of query: 871
Effective length of database: 870
Effective search space:   757770
Effective search space used:   757770
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 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