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_226952246.1 SWIT_RS10215 indolepyruvate ferredoxin oxidoreductase family protein

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



>NCBI__GCF_000016765.1:WP_226952246.1
          Length = 1142

 Score = 1006 bits (2600), Expect = 0.0
 Identities = 546/1129 (48%), Positives = 721/1129 (63%), Gaps = 27/1129 (2%)

Query: 21   LTGTQALTRLPMLQHQRDQARGLNTGGFISGYRGSPLGGLDKSLWEARDYLKQHAIHFQP 80
            L+GTQAL R  + Q + D+ARG NT GF+SGYRGSP G +D  LW+A++ L+ H+I FQP
Sbjct: 15   LSGTQALVRGMIAQAEDDRARGWNTAGFVSGYRGSPFGNVDLELWQAQEALEAHSILFQP 74

Query: 81   GVNEELAATAVWGSQQTNLFPGAKYDGVFAMWYGKGPGVDRAGDVFKHANAAGVSPQGGV 140
            G+NE++AATA WG+QQ  L    +Y+GVFA WYGKGPGVDR+GDVFKH N AG S +GGV
Sbjct: 75   GLNEDMAATACWGTQQVPLMENPRYEGVFAFWYGKGPGVDRSGDVFKHGNLAGTSAKGGV 134

Query: 141  LLLAGDDHGCKSSTLPHQSEHAFIAASIPVLNPANVQEILDYGIIGWELSRYSGCWVALK 200
            +LLAGDDHG KSS+  HQSEH F+AASIPV NP++++E  +Y  +   +SR++G W+  K
Sbjct: 135  VLLAGDDHGAKSSSTAHQSEHMFVAASIPVFNPSSIEEYFEYLPVAVSMSRFAGTWIGFK 194

Query: 201  TIAENVDSSAVVEVDPLR--VQTRIPEDFELPEDGVHIRWPDPPLAQEKRLNLYKIYAAR 258
               E V++SAV+   PLR   +T +  + E P  G HI     PLAQE+ L  Y++ AAR
Sbjct: 195  CATEIVEASAVL---PLRRPERTLVLPEVEAPSGGYHIATQFAPLAQEESLYRYRLPAAR 251

Query: 259  AFARANNLNRVMLDSPNPRLGIITTGKSYLDVRQALDDLGLDEALCASVGLRVLKVGMSW 318
            AF  AN L+RV LDSP   LGII  GK+++DV +AL  LGLD    A++G+R+LK  ++W
Sbjct: 252  AFLAANALDRVTLDSPRRMLGIIAPGKAHVDVHEALRLLGLDGERAAALGIRILKPLVTW 311

Query: 319  PLEPVSVHEFAQGLDEILVVEEKRSIIEDQLTGQLYNWPVSKRPRVVGEFDEQGNSLLPN 378
            PL+P +   F  G  E+LVVEEKRS++E QL   L   P ++RP + G+    G  LL  
Sbjct: 312  PLDPAAARPFVAGHREVLVVEEKRSLVEWQLAQILLGIPDAQRPALSGKTTPAGAPLLNE 371

Query: 379  LSELTPAMIARVIAKRLAPIYTSDSIQARLAFLAAKEKALAARSYSTVRTPHYCSGCPHN 438
              ELT   +A  +A RL  +   D+           E A A  +    R P +CSGCPHN
Sbjct: 372  YGELTATSVALALADRLEALDLLDAGLREARERIRAEAAQARGAGPVARAPMFCSGCPHN 431

Query: 439  SSTKVPEGSRASAGIGCHYMVQWM-DRRTETFTQMGGEGVNWIGQAPFTDTPHMFQNLGD 497
             ST+VPEGS A  GIGCH M  W+ D RT   T MGGEG  W+G APF    H+FQN+GD
Sbjct: 432  RSTRVPEGSEALGGIGCHGMAMWIPDLRTRPSTHMGGEGGTWLGIAPFGGPRHIFQNMGD 491

Query: 498  GTYFHSGSLAVRAAVAAGVNVTYKILYNDAVAMTGGQPIDGELRVDQLSRQIFHEGVKRI 557
            GTY HSG LA+RAA+AA VN+TYKIL N AVAMTGGQP++G      ++RQ   EG +++
Sbjct: 492  GTYAHSGLLAIRAAIAANVNITYKILCNSAVAMTGGQPVEGSPDAGIIARQTLAEGARKV 551

Query: 558  ALVSDEPDKYPSRDTFAPITSFHHRRELDAVQRELREFKGVSVIIYDQTCATEKRRRRKR 617
             LVS++PD++P       +   HHR  L  +QRELRE +GV+V++YDQ CA E+RR RKR
Sbjct: 552  VLVSEDPDRFPDMPAGIEV---HHRDALMRIQRELREIEGVTVLVYDQGCAAERRRLRKR 608

Query: 618  GKMEDPAKRAFINPAVCEGCGDCGEKSNCLAVLPLETELGRKREIDQNACNKDFSCVEGF 677
            G+  D   R FIN  VCEGCGDC  KS+C++VLPL+TELG KR+IDQ  CNKD++CVEGF
Sbjct: 609  GEYPDLPIRTFINSDVCEGCGDCNSKSSCVSVLPLQTELGVKRQIDQENCNKDYTCVEGF 668

Query: 678  CPSFVTVHGGGLRKPEAVAGGI----EAATLPEPQHPTLDRPWNVLIPGVGGSGVTTLGA 733
            CPSF+TV GG LRK  + A  +    E    P P   + D  +N+++ G+GG+GV TLGA
Sbjct: 669  CPSFITVTGGKLRKAASSADLLTTLGERLVEPAPAALSAD-SFNIVLAGIGGTGVITLGA 727

Query: 734  LLGMAAHLEGKGCTVLDQAGLAQKFGPVTTHVRIAAKQS-DIYAVRIAAGEADLLLGCDL 792
             L  AA LEG+     D  G++QK G V +H+R     S + +  RI   + DLL+GCD 
Sbjct: 728  TLARAAWLEGQKVLTFDVTGVSQKNGAVFSHIRFLGDGSEEDFRPRIPREQLDLLVGCDA 787

Query: 793  IVAAGDESLTRLNEQISNAVVNSHESATAEFTRNPDAQVPGAAMRQAISDAVGADKTHFV 852
            I A   E +  L+   + AV+N+    TA F R+P   +      + + D +     H  
Sbjct: 788  IAATAPEVVQLLSPGRTQAVLNADVIPTAVFQRDPGFDMSFQRFGRVVGDVLDDRAVHRA 847

Query: 853  DATRLATRLLGDSIATNLFLLGFAYQQGLLPISAEAIEKAIELNGVSAKLNLQAFRWGRR 912
                +A R+LG     N+F+LGFA+Q+GLLP+ +EA+E+A    G + K NL AFR GR 
Sbjct: 848  SPGPVAARILGTGPLLNIFMLGFAFQRGLLPLRSEAMERAFS-EGRNGKGNLLAFRLGRM 906

Query: 913  AVLEREAVEQL----ARPVDMVEPICKTLEEIVDWRVDFLTRYQSAGLARRYRQLVERVR 968
            A  +    ++L      PV + E     LE  +    + LT YQ    A RY + V RV 
Sbjct: 907  AAQDPATFDKLVGAEVAPVPLTE---LPLEAAIQRCRELLTSYQDRAYADRYERFVRRVA 963

Query: 969  DADSADDLALSKAVARYYFKLLAYKDEYEVARLYSEPEFRQQLEAQFEGDYKLQFHLAPA 1028
              D   D+A  +AVA   FKL+ YKDEYEVARL++ PE RQ+L+  FEG Y+L F+LAP 
Sbjct: 964  AGDPRGDVA--RAVALNLFKLMRYKDEYEVARLHASPELRQRLDRMFEGPYRLSFNLAPP 1021

Query: 1029 WLAKRDPVTGEPRKRELGPWVLNLFGVLAKFRFLRGTPLDPFGYGHDRRVERQLISEYEK 1088
             L       GEPRKR  G W+++ F +L  F+FLRGTP DPF YG DR++ER+LI++Y  
Sbjct: 1022 ILPLGRTDAGEPRKRRFGGWMMSAFRLLRHFKFLRGTPFDPFAYGADRKLERRLIADYRG 1081

Query: 1089 TVDELLAQLKPTNYRTAVAIAALPEQIRGYGPVKERSI--AKARQQEKL 1135
             ++ELL +L   +Y +AVAIAALPE IRGYGPVKER++  A AR+QE L
Sbjct: 1082 WIEELLPRLDRVDYASAVAIAALPEDIRGYGPVKERNVEAALARRQELL 1130


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: 3069
Number of extensions: 153
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 1156
Length of database: 1142
Length adjustment: 46
Effective length of query: 1110
Effective length of database: 1096
Effective search space:  1216560
Effective search space used:  1216560
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