Alignments for a candidate for ofo in Chromobacterium vaccinii MWU205

GapMind for catabolism of small carbon sources

Alignments for a candidate for ofo in Chromobacterium vaccinii MWU205

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_046158511.1 VL52_RS19015 indolepyruvate ferredoxin oxidoreductase family protein

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



>NCBI__GCF_000971335.1:WP_046158511.1
          Length = 1161

 Score = 1340 bits (3467), Expect = 0.0
 Identities = 668/1148 (58%), Positives = 846/1148 (73%), Gaps = 20/1148 (1%)

Query: 1    MSLAEIRLDDKYRLATGHLYLTGTQALTRLPMLQHQRDQARGLNTGGFISGYRGSPLGGL 60
            MS+    L++KY   TG + +TG QAL RLPMLQ + D+A GLNT G+++GYRGSPLG +
Sbjct: 1    MSIRHADLEEKYTAPTGQVLMTGIQALVRLPMLQQELDRAAGLNTAGYVTGYRGSPLGNV 60

Query: 61   DKSLWEARDYLKQHAIHFQPGVNEELAATAVWGSQQTNLFPGAKYDGVFAMWYGKGPGVD 120
            D+++ +A+ +L  H + F PG+NE+LAATAVWG+QQ N+F GAKYDGV+++WYGKGPGVD
Sbjct: 61   DQTMIKAKKHLDAHNVVFHPGLNEDLAATAVWGTQQVNIFEGAKYDGVYSLWYGKGPGVD 120

Query: 121  RAGDVFKHANAAGVSPQGGVLLLAGDDHGCKSSTLPHQSEHAFIAASIPVLNPANVQEIL 180
            R+GDV KH NAAG S  GGVLL+ GDDH  KSST PHQS+H   A+ IPVL+P+ VQE+L
Sbjct: 121  RSGDVLKHGNAAGTSKHGGVLLVCGDDHAAKSSTFPHQSDHILAASMIPVLSPSGVQEVL 180

Query: 181  DYGIIGWELSRYSGCWVALKTIAENVDSSAVVEVDPLRVQTRIPEDFELPEDGVHIRWPD 240
            D G+ GW +SRYSGCWV++K I + V+SSA+V++ P R++ +IP+DF LPEDG++IRWPD
Sbjct: 181  DLGLHGWAMSRYSGCWVSIKAITDTVESSAIVDITPERLEFKIPKDFPLPEDGLNIRWPD 240

Query: 241  PPLAQEKRLNLYKIYAARAFARANNLNRVMLDSPNPRLGIITTGKSYLDVRQALDDLGLD 300
             PLAQEKR+  +++YAA A+AR N LNR+ LDSP PRLGIIT GKSYLDV QALDDLG+ 
Sbjct: 241  TPLAQEKRVLHHRLYAALAYARENKLNRITLDSPKPRLGIITCGKSYLDVMQALDDLGIS 300

Query: 301  EALCASVGLRVLKVGMSWPLEPVSVHEFAQGLDEILVVEEKRSIIEDQLTGQLYNWPVSK 360
            EA  A +GLR+ KVGM WPLEP  V +FAQGL+EILVVEEKR IIE QL  QLYNW    
Sbjct: 301  EAQAADIGLRIFKVGMVWPLEPEGVRQFAQGLEEILVVEEKRQIIEYQLKEQLYNWRDDI 360

Query: 361  RPRVVGEFDEQ-------GNSLLPNLSELTPAMIARVIAKRLAPIYTSDSIQARLAFLAA 413
            RPRVVG+F E+       G+ LLP   ELTPAMIAR IA RLA I+ S  I  RL F   
Sbjct: 361  RPRVVGKFAEKGEWALPHGDWLLPAAGELTPAMIARAIANRLALIFDSPVIHDRLKFYDD 420

Query: 414  KEKALAARSYSTVRTPHYCSGCPHNSSTKVPEGSRASAGIGCHYMVQWMD-RRTETFTQM 472
            KE  L     S  R PHYCSGCPHN+STK+PEGSRA AGIGCHYM  W+    T+TFTQM
Sbjct: 421  KEAQLVQPRESIARVPHYCSGCPHNTSTKLPEGSRAVAGIGCHYMAHWISPENTKTFTQM 480

Query: 473  GGEGVNWIGQAPFTDTPHMFQNLGDGTYFHSGSLAVRAAVAAGVNVTYKILYNDAVAMTG 532
            GGEG+ W+GQAPFT T H+F NLGDGTYFHSG LA+RAAVA  VN+TYKILYNDAVAMTG
Sbjct: 481  GGEGITWLGQAPFTTTRHIFTNLGDGTYFHSGILAIRAAVAGKVNITYKILYNDAVAMTG 540

Query: 533  GQPIDGELRVDQLSRQIFHEGVKRIALVSDEPDKYPSRDTFAPITSFHHRRELDAVQREL 592
            GQ +DG L V  ++RQ+  EGVKRI + SD+PDKY +    AP     HRRELD VQREL
Sbjct: 541  GQHVDGYLDVPMMTRQLAAEGVKRIVITSDDPDKYQNAQGLAPGIDVFHRRELDRVQREL 600

Query: 593  REFKGVSVIIYDQTCATEKRRRRKRGKMEDPAKRAFINPAVCEGCGDCGEKSNCLAVLPL 652
            R+ +GV+++I+DQTCA EKRRRRKR +  DPAKRAFIN  VCEGCGDC +KS CL+VLP+
Sbjct: 601  RDIEGVTILIHDQTCAAEKRRRRKRNEFPDPAKRAFINERVCEGCGDCSKKSGCLSVLPV 660

Query: 653  ETELGRKREIDQNACNKDFSCVEGFCPSFVTVHGGGLRKPEAVAGGI-EAATLPEPQHPT 711
            ET LGRKR+IDQ++CNKD+SCVEGFCPSFVTV GG LRKP   +  + +   LP P+ P 
Sbjct: 661  ETPLGRKRKIDQSSCNKDYSCVEGFCPSFVTVEGGKLRKPAGASADLAKMPALPMPKIPA 720

Query: 712  LDRPWNVLIPGVGGSGVTTLGALLGMAAHLEGKGCTVLDQAGLAQKFGPVTTHVRIAAKQ 771
            L  P+ +++ GVGG+GV T+G +LGMAA+L+ KG TVLD AGLAQK G V +HVRIA  Q
Sbjct: 721  LHEPFGIMVTGVGGTGVVTIGQVLGMAAYLDNKGVTVLDMAGLAQKGGSVWSHVRIADSQ 780

Query: 772  SDIYAVRIAAGEADLLLGCDLIVAAGDESLTRLNEQISNAVVNSHESATAEFTRNPDAQV 831
              ++AVRIAAG+A+L+LGCDL+V A +E+L ++ +  S+A+VNS+ES T+ F +NPD + 
Sbjct: 781  DKLHAVRIAAGDANLVLGCDLVVTAAEEALAKMRDGFSHAIVNSYESPTSGFLKNPDIRY 840

Query: 832  PGAAMRQAISDAVGADKTHFVDATRLATRLLGDSIATNLFLLGFAYQQGLLPISAEAIEK 891
            P  AM+ AI +AVGA +   V+A +LAT L+GD+IA N+F+LG+ +Q+GL+P+S EAI +
Sbjct: 841  PAKAMKDAIVEAVGAGRFSEVNANKLATALMGDAIAANMFMLGYGWQKGLVPVSLEAIME 900

Query: 892  AIELNGVSAKLNLQAFRWGRRAVLEREAVEQLARPVDMVEPICK-TLEEIVDWRVDFLTR 950
            A+ LNG + K N  AF WGR A  +   VE L  P  +V+ + + T + +V  R   L  
Sbjct: 901  AVRLNGAAVKFNQDAFTWGRHAAQDLARVEALVSPTAVVQFVPRETPDAVVHHRSTLLAA 960

Query: 951  YQSAGLARRYRQLVERVRDADSA---DDLALSKAVARYYFKLLAYKDEYEVARLYSEPEF 1007
            YQ+  LA RY+ LV++VR A+ A      AL+ A AR Y  LLAYKDEYEVARLYS+ EF
Sbjct: 961  YQNGALAERYKALVQQVRQAEEAAQPGSTALTLAAARAYHHLLAYKDEYEVARLYSDGEF 1020

Query: 1008 RQQLEAQFEGDYKLQFHLAPAWLAKRDPVTGEPRKRELGPWVLNLFGVLAKFRFLRGTPL 1067
            ++++ AQF+GDYKL+FH+  AWL +     G+PRK  +G W++    VLAK RFLRGT L
Sbjct: 1021 QREVAAQFDGDYKLRFHIGVAWLTR-----GQPRKIAIGSWLMPAMKVLAKLRFLRGTAL 1075

Query: 1068 DPFGYGHDRRVERQLISEYEKTVDELLAQLKPTNYRTAVAIAALPEQIRGYGPVKERSI- 1126
            DPF +  DR++ERQLI+E+E+ +  LLA+L P     AV      E +RG+G +K  +  
Sbjct: 1076 DPFAWQDDRKLERQLIAEFEQELPALLAKLTPDTLPRAVEWMKTWEGVRGFGHIKLANYR 1135

Query: 1127 -AKARQQE 1133
             AK RQ E
Sbjct: 1136 QAKTRQAE 1143


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: 3137
Number of extensions: 134
Number of successful extensions: 7
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: 1161
Length adjustment: 47
Effective length of query: 1109
Effective length of database: 1114
Effective search space:  1235426
Effective search space used:  1235426
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 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