Alignments for a candidate for iorAB in Paraburkholderia phymatum STM815

GapMind for catabolism of small carbon sources

Alignments for a candidate for iorAB in Paraburkholderia phymatum STM815

Align phenylpyruvate ferredoxin oxidoreductase (EC 1.2.7.8) (characterized)
to candidate WP_012404781.1 BPHY_RS27730 MFS transporter

Query= reanno::Marino:GFF880
         (1172 letters)



>NCBI__GCF_000020045.1:WP_012404781.1
          Length = 1195

 Score = 1117 bits (2888), Expect = 0.0
 Identities = 587/1166 (50%), Positives = 779/1166 (66%), Gaps = 32/1166 (2%)

Query: 13   LEDRYLRESGRVFLTGTQALVRIPLMQAALDRKQGLNTAGLVSGYRGSPLGAVDQALWQA 72
            L+D+Y  E GRV+++GTQALVR+P++Q A D K GLNTAG +SGYRGSPLGA+DQ+LW+A
Sbjct: 20   LDDKYTLEKGRVYISGTQALVRLPMLQKARDLKAGLNTAGFISGYRGSPLGALDQSLWKA 79

Query: 73   KDLLDENRIDFVPAINEDLAATILLGTQQVETDEDRQVEGVFGLWYGKGPGVDRAGDALK 132
            K  L  N I F P +NEDLAAT + GTQQ+        +GVFG+WYGKGPGVDR GD  +
Sbjct: 80   KKHLQANDIVFQPGVNEDLAATAVWGTQQINLWPGATRDGVFGMWYGKGPGVDRTGDVFR 139

Query: 133  HGTTYGSSPHGGVLVVAGDDHGCVSSSMPHQSDVAFMSFFMPTINPANIAEYLEFGLWGY 192
            H  + GS   GGVLV+AGDDH   SSS+ HQS+ AF++  +P + PAN+ EYL++GL G+
Sbjct: 140  HANSAGSDARGGVLVLAGDDHAAKSSSVAHQSEHAFIAAGIPVLYPANVQEYLDYGLHGW 199

Query: 193  ALSRYSGCWVGFKAISETVESAASVEI-PPAPDFVTPDDFTAPESGLHYRWPDLPGPQLE 251
            A+SRYSG WV  K +++ +ES AS+++ P   D VTP D+  P  GL+ RWPD P  Q  
Sbjct: 200  AMSRYSGLWVAMKCVTDVIESTASIDLDPDRVDIVTPTDYAMPAGGLNIRWPDAPLAQEA 259

Query: 252  TRIEHKLAAVQAFARANRIDRCLFDNKEARFGIVTTGKGHLDLLEALDLLGIDEDKARDM 311
              ++ K  A  A+ RANR++R + D+ + RFGI+T GK +LD+ +AL  LG+D+D    +
Sbjct: 260  RLLDEKWYAALAYIRANRLNRVVIDSDKPRFGIITAGKAYLDVRQALSDLGLDDDTCARI 319

Query: 312  GLDIYKVGMVWPLERRGILDFVHGKEEVLVIEEKRGIIESQIKEYMSEPDRPGEVLITGK 371
            GL + KVG VWPL+ +    F  G EE+LV+EEKR I+E  +KE +          I GK
Sbjct: 320  GLRVLKVGCVWPLDAQDARAFATGLEEILVVEEKRQILEYALKEELYNWREDVRPKIYGK 379

Query: 372  QDE-----------LGRPLIPYVGELSPKLVAGFLAARLGRF-FEVDFSERM------AE 413
             DE            G  L+P   ELSP L+A  +A RL R     D   RM       E
Sbjct: 380  FDERDNEGGEWSVPRGDWLLPAHYELSPALIAKAIARRLARADLPKDVRARMLARVAIIE 439

Query: 414  ISAMTTAQDPGGVKRMPYFCSGCPHNTSTKVPEGSKALAGIGCHFMASWMGRNTESLIQM 473
                  A+    V+R P+FCSGCPHNTST+VPEGS+ALAGIGCH+M+ WM R TE+  QM
Sbjct: 440  AKEREAAKPRVAVERKPWFCSGCPHNTSTRVPEGSRALAGIGCHYMSMWMDRKTETFSQM 499

Query: 474  GGEGVNWIGKSRYTGNPHVFQNLGEGTYFHSGSMAIRQAVAAGINITYKILFNDAVAMTG 533
            GGEGV WIG+  ++G+ HVF NLG+GTYFHSG +AIR A+AA  NITYK+L+NDAVAMTG
Sbjct: 500  GGEGVAWIGQMHFSGDRHVFVNLGDGTYFHSGLLAIRAAIAANANITYKVLYNDAVAMTG 559

Query: 534  GQPVDGQITVDRIAQQMAAEGVNRVVVLSDEPEKYDGHHDLFPKDVTFHDRSELDQVQRE 593
            GQPVDG +TV +IA Q+ AEG  RVV+++DEP+KY     + P  V  H R +LD VQR 
Sbjct: 560  GQPVDGVLTVPQIAHQVHAEGAKRVVIVTDEPQKY-RTGIVLPAGVDVHHRDQLDTVQRT 618

Query: 594  LRDIPGCTVLIYDQTCAAEKRRRRKRKQFPDPAKRAFINHHVCEGCGDCSVQSNCLSVVP 653
            LRDIPG TVLIYDQTCA EKRRRRKR  +PDPA+RAFIN  VCEGCGDCS QSNCLSV P
Sbjct: 619  LRDIPGTTVLIYDQTCATEKRRRRKRGTYPDPARRAFINDAVCEGCGDCSEQSNCLSVEP 678

Query: 654  RKTELGRKRKIDQSSCNKDFSCVNGFCPSFVTIEGGQLRKSRGVDTGSVLTRKLAD---I 710
              T LG KRKI+QSSCNKDFSCVNGFCPSFVT EG QLRK +             D   +
Sbjct: 679  LDTPLGTKRKINQSSCNKDFSCVNGFCPSFVTAEGAQLRKPKAAGGDKSAGAGKIDFDAL 738

Query: 711  PAPKLPEMTGSYDLLVGGVGGTGVVTVGQLITMAAHLESRGASVLDFMGFAQKGGTVLSY 770
            PAP LP +   Y +LV GVGGTGVVT+G LI MAAH+E +G +VLD  G AQKGG VLS+
Sbjct: 739  PAPSLPALAKPYGILVTGVGGTGVVTIGGLIGMAAHIEHKGVTVLDMAGLAQKGGAVLSH 798

Query: 771  VRMAPSPDKLHQVRISNGQADAVIACDLVVASSQKALSVLRPNHTRIVANEAELPTADYV 830
            V++A +P+ LH  RI+ G+A  VI CD +V++S   LS  +   T    N    PTA++V
Sbjct: 799  VQLASAPEALHATRIATGEARLVIGCDAIVSASNDVLSRTQHGVTCAAINSGATPTAEFV 858

Query: 831  LFRDADMKADKRLGLLKNAVGEDHFDQLDANGIAEKLMGDTVFSNVMMLGFAWQKGLLPL 890
                      +    L++++G D    +DAN +A  L+GDT++SN ++LGFAWQKG LPL
Sbjct: 859  KNPKWTFPGTQTEAELRDSIG-DGCAFIDANALALTLLGDTIYSNPLLLGFAWQKGWLPL 917

Query: 891  SEAALMKAIELNGVAIDRNKEAFGWGRLSAVDPSAVTDLLDDSNA--QVVEVKPEPTLDE 948
              ++L++AIELN V++++N++AF WGR  A         L    A  Q + ++   +LD 
Sbjct: 918  QLSSLLRAIELNAVSVEKNQQAFNWGRYIAQHGDDAVRALGKPAAAPQAIVMRIPESLDH 977

Query: 949  LINTRHKHLVNYQNQRWADQYRDAVAGVRKAE-ESLGETNLLLTRAVAQQLYRFMAYKDE 1007
            LI +R   L +YQN+ +A +YR  + G+R  E E  G++ L LTRA+A  L + MAYKDE
Sbjct: 978  LIASREALLKSYQNEAYARKYRRVIDGIRAKEMEFGGDSKLPLTRAIATNLAKLMAYKDE 1037

Query: 1008 YEVARLFAETDFMKEVNETFEG----DFKVHFHLAPPLLSGETDAQGRPKKRRFGPWMFR 1063
            YEVARL+A+  +++++ + FEG    D+K+ F+LAPPL + + D +G  +K+RFGPWM  
Sbjct: 1038 YEVARLYADPAYLEKLRQQFEGEPGRDYKLSFYLAPPLFA-KRDERGHLQKKRFGPWMLP 1096

Query: 1064 AFRLLAKLRGLRGTAIDPFRYSADRKLDRAMLKDYQSLVDRIGRELNASNYETFLQLAEL 1123
            AFR+LA+++GLRGTA D F  + +R+ +R ++ +Y +LVD     L +      LQLA L
Sbjct: 1097 AFRVLARMKGLRGTAFDVFGKTVERRGERQLIAEYIALVDEFCATLTSDRLAVALQLACL 1156

Query: 1124 PADVRGYGPVREQAAESIREKQTQLI 1149
            P D+RG+G V+E+  ++  +K+ +L+
Sbjct: 1157 PDDIRGFGHVKERNLQAAAKKKERLL 1182


Lambda     K      H
   0.319    0.136    0.405 

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: 3135
Number of extensions: 130
Number of successful extensions: 11
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: 1172
Length of database: 1195
Length adjustment: 47
Effective length of query: 1125
Effective length of database: 1148
Effective search space:  1291500
Effective search space used:  1291500
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 (21.7 bits)
S2: 58 (26.9 bits)

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

Downloads

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

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:

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