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_012402219.1 BPHY_RS14615 MFS transporter

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



>NCBI__GCF_000020045.1:WP_012402219.1
          Length = 1200

 Score = 1120 bits (2898), Expect = 0.0
 Identities = 576/1179 (48%), Positives = 789/1179 (66%), Gaps = 47/1179 (3%)

Query: 8    LDDYKLEDRYLRESGRVFLTGTQALVRIPLMQAALDRKQGLNTAGLVSGYRGSPLGAVDQ 67
            L    L+D+Y  E GR +++G QALVR+P++Q   DR  GLNTAG +SGYRGSPLG +D 
Sbjct: 17   LSSVTLDDKYTLERGRAYMSGIQALVRLPMLQQERDRAAGLNTAGFISGYRGSPLGGLDL 76

Query: 68   ALWQAKDLLDENRIDFVPAINEDLAATILLGTQQVETDEDRQVEGVFGLWYGKGPGVDRA 127
            +LW+AK  L  +++ F P +NEDLAAT + G+QQV      + +GVF +WYGKGPGVDR+
Sbjct: 77   SLWKAKKHLAAHQVVFQPGVNEDLAATAVWGSQQVNLYPSAKYDGVFSMWYGKGPGVDRS 136

Query: 128  GDALKHGTTYGSSPHGGVLVVAGDDHGCVSSSMPHQSDVAFMSFFMPTINPANIAEYLEF 187
            GD  KHG + GSS HGGVLV+AGDDH   SS++ HQS+  F +  +P + P+N+ EYL+F
Sbjct: 137  GDVFKHGNSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHLFKACGLPVLFPSNVQEYLDF 196

Query: 188  GLWGYALSRYSGCWVGFKAISETVESAASVEIPP-APDFVTPDDFTAPESGLHYRWPDLP 246
            GL G+A+SRYSG WV  K +++ VES+ASV+I P     + P DF  PE GL+ RWPD P
Sbjct: 197  GLHGWAMSRYSGLWVAMKCVTDVVESSASVDIDPHRTQIILPADFAMPEGGLNIRWPDPP 256

Query: 247  GPQLETRIEHKLAAVQAFARANRIDRCLFDNKEARFGIVTTGKGHLDLLEALDLLGIDED 306
              Q    +++K  A  A+ RAN++DR   D+  ARFGI+T GK +LD+ +AL  LG+D++
Sbjct: 257  LVQEARLLDYKWYAGLAYVRANKLDRVEIDSPHARFGIITGGKAYLDVRQALTDLGLDDE 316

Query: 307  KARDMGLDIYKVGMVWPLERRGILDFVHGKEEVLVIEEKRGIIESQIKEYMSEPDRPGEV 366
                +G+ +YKVG VWPLE +G   F    +E+LV+EEKR I+E  IKE +         
Sbjct: 317  TCSRIGIRLYKVGCVWPLEAQGAQAFARELQEILVVEEKRQILEYAIKEELYNWPDAQRP 376

Query: 367  LITGKQDE-----------LGRPLIPYVGELSPKLVAGFLAARLGRF-FEVDFSERMAEI 414
             + GK DE           +G  L+P   ELSP L+A  +A RL +F    D   R+A  
Sbjct: 377  RVFGKFDEKDGAGGEWSVPMGNWLLPAHYELSPALIAKAIATRLDKFDLPSDVRARIAAR 436

Query: 415  SAMTTAQDPG------GVKRMPYFCSGCPHNTSTKVPEGSKALAGIGCHFMASWMGRNTE 468
             A+  A++         ++R P+FCSGCPHNTST VPEGS+A+AGIGCH+M  WM R+T 
Sbjct: 437  IAVIEAKEKALARPKVAIERKPWFCSGCPHNTSTNVPEGSRAMAGIGCHYMTVWMDRSTS 496

Query: 469  SLIQMGGEGVNWIGKSRYTGNPHVFQNLGEGTYFHSGSMAIRQAVAAGINITYKILFNDA 528
            +  QMGGEGV W+G++ +T + HVF NLG+GTYFHSG +AIR A+A+  NITYKIL+NDA
Sbjct: 497  TFSQMGGEGVAWVGQAPFTNDKHVFANLGDGTYFHSGLLAIRAAIASKANITYKILYNDA 556

Query: 529  VAMTGGQPVDGQITVDRIAQQMAAEGVNRVVVLSDEPEKYDGHHDLFPKDVTFHDRSELD 588
            VAMTGGQPVDG +TV +I  Q+AAEG  ++V+++DEP+KYD +  L P  +  H R +LD
Sbjct: 557  VAMTGGQPVDGTLTVPQITHQLAAEGAKKIVIVTDEPQKYDANVGLAP-GIDIHHRDKLD 615

Query: 589  QVQRELRDIPGCTVLIYDQTCAAEKRRRRKRKQFPDPAKRAFINHHVCEGCGDCSVQSNC 648
             VQRELRDI G T+LIYDQTCA EKRRRRKR  +PDPAKR  IN  VCEGCGDCSVQSNC
Sbjct: 616  DVQRELRDIEGTTILIYDQTCATEKRRRRKRGAYPDPAKRVVINEAVCEGCGDCSVQSNC 675

Query: 649  LSVVPRKTELGRKRKIDQSSCNKDFSCVNGFCPSFVTIEGGQLRKSRGVDTGSVLTRKLA 708
            LSV P +TE G KR+I+QS+CNKD+SC+ GFCPSFVT+EGGQLRK +      + +  + 
Sbjct: 676  LSVEPLETEYGTKRQINQSTCNKDYSCLKGFCPSFVTVEGGQLRKPK---ASGLASEAVP 732

Query: 709  DIPAPKLPEMTGSYDLLVGGVGGTGVVTVGQLITMAAHLESRGASVLDFMGFAQKGGTVL 768
             +P P++P +T  Y +LV GVGGTGVVT+G L+ MAAHLES+G +VLD  G AQKGG V+
Sbjct: 733  PVPDPEIPAITQPYGVLVTGVGGTGVVTIGALLGMAAHLESKGVTVLDVTGLAQKGGAVM 792

Query: 769  SYVRMAPSPDKLHQVRISNGQADAVIACDLVVASSQKALSVLRPNHTRIVANEAELPTAD 828
            S+V++A  P  +H  RI+ G+A+ VI CD +V +S + +S ++   TR+V N A  PTA+
Sbjct: 793  SHVQIANQPADIHATRIAMGEANLVIGCDSIVTASDECVSRMQSGRTRVVLNSAPTPTAE 852

Query: 829  YV-----LFRDADMKADKRLGLLKNAVGEDHFDQLDANGIAEKLMGDTVFSNVMMLGFAW 883
            ++      F  A   AD     ++ A G+D    +DAN  A  L+GD +++N  +LG+AW
Sbjct: 853  FIKNPNWRFPGASADAD-----IRAAAGDDSVSAVDANRFAVALLGDAIYTNPFVLGYAW 907

Query: 884  QKGLLPLSEAALMKAIELNGVAIDRNKEAFGWGRLSAVDPSAVTDL------LDDSN--- 934
            QKG LPL+  +L++AIELN V +++N+ AF WGR +A D +AV  L       DD N   
Sbjct: 908  QKGWLPLTHESLIRAIELNAVQVEKNRAAFEWGRRAAHDLAAVRKLANLQDGTDDGNTNA 967

Query: 935  --AQVVEVKPEPTLDELINTRHKHLVNYQNQRWADQYRDAVAGVRKAEESLG--ETNLLL 990
              +++V +     LD LI+ R ++LV YQN  +A +YR  V  VR AE  LG  +  + L
Sbjct: 968  AGSKIVSLHTPKALDTLIDKRAQYLVAYQNDAYATRYRKLVEEVRAAETKLGAADGQMPL 1027

Query: 991  TRAVAQQLYRFMAYKDEYEVARLFAETDFMKEVNETFEGDFKVHFHLAPPLLSGETDAQG 1050
            T AVA+ L++ MAYKDEYEVARL+++  F++++   FEGD+K+ FHLAPP  +   D  G
Sbjct: 1028 TEAVAKNLHKLMAYKDEYEVARLYSDPAFIEKLKANFEGDWKLRFHLAPP-ATATKDTHG 1086

Query: 1051 RPKKRRFGPWMFRAFRLLAKLRGLRGTAIDPFRYSADRKLDRAMLKDYQSLVDRIGRELN 1110
               K+++GPWM  A  +LAK++ LRGTA+D F  + +R+ +RA++ +Y+ LV  +   L 
Sbjct: 1087 HLVKKQYGPWMLNAMHVLAKMKFLRGTALDMFGKTEERRTERALIVEYEVLVRELIGGLT 1146

Query: 1111 ASNYETFLQLAELPADVRGYGPVREQAAESIREKQTQLI 1149
            A      ++LA LP  +RGYG V++   +S+R K   L+
Sbjct: 1147 AEKRALAIELANLPDGIRGYGHVKDNNLKSVRAKWASLL 1185


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: 3128
Number of extensions: 138
Number of successful extensions: 10
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: 1200
Length adjustment: 47
Effective length of query: 1125
Effective length of database: 1153
Effective search space:  1297125
Effective search space used:  1297125
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: 59 (27.3 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