Alignments for a candidate for ofo in Rhizorhabdus wittichii RW1

GapMind for catabolism of small carbon sources

Alignments for a candidate for ofo in Rhizorhabdus wittichii RW1

Align branched-chain ketoacid ferredoxin reductase (EC 1.2.7.7) active on 4-methyl-2-oxopentanoate, (S)-3-methyl-2-oxopentanoate, or 3-methyl-2-oxobutanoate (characterized)
to candidate WP_011952672.1 SWIT_RS09265 indolepyruvate ferredoxin oxidoreductase family protein

Query= reanno::psRCH2:GFF3452
         (1156 letters)



>NCBI__GCF_000016765.1:WP_011952672.1
          Length = 1171

 Score = 1151 bits (2977), Expect = 0.0
 Identities = 610/1157 (52%), Positives = 781/1157 (67%), Gaps = 29/1157 (2%)

Query: 3    LAEIRLDDKYRLATGHLYLTGTQALTRLPMLQHQRDQARGLNTGGFISGYRGSPLGGLDK 62
            L +  LDD+YR  +G +YL+G+QAL RLPMLQ  RD A G NT GFISGY GSPLGG D 
Sbjct: 12   LHDYALDDRYRRTSGRVYLSGSQALVRLPMLQRVRDLAEGRNTAGFISGYTGSPLGGYDT 71

Query: 63   SLWEARDYLKQHAIHFQPGVNEELAATAVWGSQQTNLFPGAKYDGVFAMWYGKGPGVDRA 122
            +L  A+  L  H I FQPG+NEEL ATAVWGSQQT+LF  A+YDGVFA+WYGKGPG+DRA
Sbjct: 72   ALKAAKKELDAHHIVFQPGLNEELGATAVWGSQQTDLFGEARYDGVFALWYGKGPGLDRA 131

Query: 123  GDVFKHANAAGVSPQGGVLLLAGDDHGCKSSTLPHQSEHAFIAASIPVLNPANVQEILDY 182
            GD  KH N +G S  GGVL+LAGDDHG KSST  HQS+H FI   IP  NPA+VQ+ LDY
Sbjct: 132  GDAIKHGNYSGSSKHGGVLVLAGDDHGAKSSTTAHQSDHGFIHYGIPYFNPASVQDYLDY 191

Query: 183  GIIGWELSRYSGCWVALKTIAENVDSSAVVEVDPLRVQTRIPEDFELPEDGVHIRWPDPP 242
            G+ G  LSR++GCWV +K + + ++SSA V++  +      PE     + G + RW   P
Sbjct: 192  GLHGIALSRHAGCWVGMKCVTDTIESSASVDISAMEAPILPPEAEAQGQAGRNARWGVHP 251

Query: 243  LAQEKRLNLYKIYAARAFARANNLNRVMLDSPNPRLGIITTGKSYLDVRQALDDLGLDEA 302
            +  E+     ++ A +AF +AN LN  ++ + +  LGI+T GK++LDV QAL++LGLD  
Sbjct: 252  VLAEQSHYQRRLPAVQAFVKANRLNHPVIHAEDGLLGIVTGGKAWLDVMQALEELGLDRD 311

Query: 303  LCASVGLRVLKVGMSWPLEPVSVHEFAQGLDEILVVEEKRSIIEDQLTGQLYNWPVSKRP 362
             C   G+ V KV M WPLEP  + +FA+    ILVVEEKR IIE QL G   N      P
Sbjct: 312  GCRRHGVGVFKVAMPWPLEPDLIADFARAYRTILVVEEKRPIIEQQLAGLFVN--DRSAP 369

Query: 363  RVVGEFDEQGNSLLPNLSELTPAMIARVIAKRLAPIYTSDSIQARLAFLAAKEKALAARS 422
             ++G+ DE G+ L+P++ EL   ++A  I   LA +       AR A  A      A ++
Sbjct: 370  ILIGKNDEAGSPLIPSVGELNAPLLAAAIGSTLARLGAGPGPAARSAPTATG----AGQA 425

Query: 423  YSTVRTPHYCSGCPHNSSTKVPEGSRASAGIGCHYMVQWM-DRRTETFTQMGGEGVNWIG 481
               VR P +C+GCPHN ST+VP+GS A  GIGCH M  ++ +R T T  QMGGEG  WIG
Sbjct: 426  AGLVRLPSFCAGCPHNGSTRVPQGSVAFGGIGCHGMATFLPERNTPTLFQMGGEGAPWIG 485

Query: 482  QAPFTDTPHMFQNLGDGTYFHSGSLAVRAAVAAGVNVTYKILYNDAVAMTGGQPIDGELR 541
             +PFT+  H+FQNLGDGTY+HSG LA+RAAVAA VN+TYKIL NDA+AMTGGQ I+G +R
Sbjct: 486  LSPFTERKHIFQNLGDGTYYHSGLLAIRAAVAAKVNITYKILVNDAIAMTGGQVIEGSVR 545

Query: 542  VDQLSRQIFHEGVKRIALVSDEPDKYPSRDTFAPITSFHHRRELDAVQRELREFKGVSVI 601
            VD L+RQ+  EGV+RIA+VSD+ DKY +   FAP  + HHR +L AVQ ELRE +GVS++
Sbjct: 546  VDALTRQVHAEGVRRIAVVSDDIDKYRAGHDFAPGVTIHHRDDLAAVQEELREVEGVSIL 605

Query: 602  IYDQTCATEKRRRRKRGKMEDPAKRAFINPAVCEGCGDCGEKSNCLAVLPLETELGRKRE 661
            +Y+Q CATE RRRRKRGK EDP +R FINP VCEGCGDCG +SNC+A+ P+ET  GRKR 
Sbjct: 606  VYEQYCATELRRRRKRGKAEDPDRRIFINPRVCEGCGDCGVQSNCIAIEPVETGFGRKRR 665

Query: 662  IDQNACNKDFSCVEGFCPSFVTVHG---------GGLRKPEAVAGGIEAATLPEPQHPTL 712
            I+Q+ACNKDFSC +G+CPSFVTVHG         G    P A A    AA LP P+   +
Sbjct: 666  INQSACNKDFSCTKGYCPSFVTVHGAKPRRRGSSGAAALPPAAAE--LAARLPTPKVAPV 723

Query: 713  DRPWNVLIPGVGGSGVTTLGALLGMAAHLEGKGCTVLDQAGLAQKFGPVTTHVRIAAKQS 772
            D P+++L+ G+GG+GV T+GALLGMAAHLEGKGC+VLD AGLAQ+ GPVT+HVRIA +  
Sbjct: 724  DAPFSLLVTGIGGAGVVTVGALLGMAAHLEGKGCSVLDVAGLAQRNGPVTSHVRIARRPE 783

Query: 773  DIYAVRIAAGEADLLLGCDLIVAAGDESLTRLNEQISNAVVNSHESATAEFTRNPDAQVP 832
            D++A RI    ADL+LGCD++V AG E+ +++  + S AVVN+  + T+ F  NPD  + 
Sbjct: 784  DLHATRIVT--ADLVLGCDIVVTAGQEATSKMVAERSRAVVNTRVAPTSAFASNPDLNLD 841

Query: 833  GAAMRQAISDAVGAD-KTHFVDATRLATRLLGDSIATNLFLLGFAYQQGLLPISAEAIEK 891
              AM   I  ++G D    FVDA RLA  L+G+ IATNLFL+G+A Q+G +P+  +++ +
Sbjct: 842  AGAMVDRIRASLGDDANAAFVDAGRLADALMGNEIATNLFLVGYAIQKGWMPVGIDSVLR 901

Query: 892  AIELNGVSAKLNLQAFRWGRRAVLEREAVEQLARPV-----DMVEPICKTLEEIVDWRVD 946
            AI+LNGVS ++N  A  WGR A  +  AV+  A  V     + + P  + L ++V     
Sbjct: 902  AIDLNGVSVEMNRTALLWGRIAAEDLAAVQACAFGVGSGEGEALPPQEEALGDLVARLAA 961

Query: 947  FLTRYQSAGLARRYRQLVERVRDADSA---DDLALSKAVARYYFKLLAYKDEYEVARLYS 1003
             L  YQ AG ARRYR LV RVR AD        ALSKAVARY  KL+AYKDEYEVARLYS
Sbjct: 962  DLAAYQDAGYARRYRALVARVRSADGGFPERQAALSKAVARYLHKLMAYKDEYEVARLYS 1021

Query: 1004 EPEFRQQLEAQFEGDYKLQFHLAPAWLAKRDPVTGEPRKRELGPWVLNLFGVLAKFRFLR 1063
            +  FR+ LE  FEGD +L+FH+AP  L KRDP TG  RKR  G   + L+ +LAK +FLR
Sbjct: 1022 DGAFRRALEEAFEGDLRLEFHMAPPLLQKRDPRTGRYRKRTFGRGTMRLYALLAKLKFLR 1081

Query: 1064 GTPLDPFGYGHDRRVERQLISEYEKTVDELLAQLKPTNYRTAVAIAALPEQIRGYGPVKE 1123
            GTP DPFG    RR ER LI  YE  ++E+L  L    Y  AV IA+ PE IRGY  VK+
Sbjct: 1082 GTPFDPFGRSAHRREERALIVHYEGLIEEVLRHLDAETYDLAVEIASYPELIRGYDSVKD 1141

Query: 1124 RSIAKARQQEKLLREQL 1140
              + +AR + + LR++L
Sbjct: 1142 EHLGRARARLEELRQRL 1158


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: 3102
Number of extensions: 141
Number of successful extensions: 8
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: 1156
Length of database: 1171
Length adjustment: 47
Effective length of query: 1109
Effective length of database: 1124
Effective search space:  1246516
Effective search space used:  1246516
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: 58 (26.9 bits)

This GapMind analysis is from Apr 09 2024. 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 2024 update 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