Alignments for a candidate for ofo in Ruegeria conchae TW15

GapMind for catabolism of small carbon sources

Alignments for a candidate for ofo in Ruegeria conchae TW15

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_010437962.1 G7G_RS0102470 indolepyruvate ferredoxin oxidoreductase family protein

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



>NCBI__GCF_000192475.1:WP_010437962.1
          Length = 1131

 Score = 1043 bits (2696), Expect = 0.0
 Identities = 546/1130 (48%), Positives = 755/1130 (66%), Gaps = 16/1130 (1%)

Query: 7    RLDDKYRLATGHLYLTGTQALTRLPMLQHQRDQARGLNTGGFISGYRGSPLGGLDKSLWE 66
            +LDD+Y L  G ++LTGTQAL R+ M Q +RD+  GLNT GF+SGYRGSPLGGLD  LW 
Sbjct: 12   QLDDRYSLTQGRVFLTGTQALARIMMDQARRDRQAGLNTSGFVSGYRGSPLGGLDLELWR 71

Query: 67   ARDYLKQHAIHFQPGVNEELAATAVWGSQQTNLFPGAKYDGVFAMWYGKGPGVDRAGDVF 126
            A++ L    I F P VNE+L ATAV G+QQ  L P  + +G+F+MWYGKGPGVDR+GD  
Sbjct: 72   AKERLIADRITFMPAVNEDLGATAVLGAQQATLDPHCEVEGIFSMWYGKGPGVDRSGDAL 131

Query: 127  KHANAAGVSPQGGVLLLAGDDHGCKSSTLPHQSEHAFIAASIPVLNPANVQEILDYGIIG 186
            KH NA G +P+GGVL++AGDDHGC SS++PHQS+ AF+A  +P LNPA+V+E L++G  G
Sbjct: 132  KHGNAYGSAPKGGVLVVAGDDHGCVSSSMPHQSDVAFMAWFMPTLNPASVEEYLEFGEYG 191

Query: 187  WELSRYSGCWVALKTIAENVDSSAVVEVDPLRVQTRIPEDFELPEDGVHIRWPDPPLAQE 246
            + LSR+SG WV  K I+E V+S+  V++ P R  T +P   +LPE G+H+R  D P  + 
Sbjct: 192  FALSRFSGTWVGFKAISETVESARSVDLRPDRSFT-LPR-IDLPERGLHVRTADLPSPEI 249

Query: 247  KRLNLYKIYAARAFARANNLNRVMLDSPNPRLGIITTGKSYLDVRQALDDLGLDEALCAS 306
            +    +K+ A RAFA  N ++R + D  N + G +TTGK +LD+ +AL  LGLDEA C  
Sbjct: 250  ETRIQHKLRAVRAFAEENPIDRRIYDIDNAKFGFVTTGKGHLDLMEALRLLGLDEAACRR 309

Query: 307  VGLRVLKVGMSWPLEPVSVHEFAQGLDEILVVEEKRSIIEDQLTGQLYNWPVSKRPRVVG 366
            +G+ + KVGM WPL   +   F +G  E+LVVEEKR IIE Q     Y+WP  K  ++VG
Sbjct: 310  LGIDIYKVGMVWPLARRNALRFVKGKAEVLVVEEKRGIIESQFKEYFYDWPGDKPHKMVG 369

Query: 367  EFDEQGNSLLPNLSELTPAMIARVIAKRLAPIYTSDSIQARLAFLAAKEKALAARSYSTV 426
            ++D  G  L+P   EL+P M+A ++A RL   +  +++ A+   L          S +T 
Sbjct: 370  KYDSHGEPLIPWTGELSPLMLAPIVAARLDTFFPEENLPAKARALTETPPPEINVSGAT- 428

Query: 427  RTPHYCSGCPHNSSTKVPEGSRASAGIGCHYMVQWMDRRTETFTQMGGEGVNWIGQAPFT 486
            RTP++CSGCPHN+STKVP+GS A++GIGCH M  WMDR T  + QMGGEGV  +  + F 
Sbjct: 429  RTPYFCSGCPHNTSTKVPDGSTAASGIGCHVMASWMDRETVGYAQMGGEGVPHVVASQFN 488

Query: 487  DTPHMFQNLGDGTYFHSGSLAVRAAVAAGVNVTYKILYNDAVAMTGGQPIDGELRVDQLS 546
               H+FQNLG+GT++HSGSLA+R AVAAG N+TYKILYNDAVAMTGGQP+DG + V  ++
Sbjct: 489  GGKHIFQNLGEGTWYHSGSLAIRQAVAAGTNITYKILYNDAVAMTGGQPVDGPVSVAGIA 548

Query: 547  RQIFHEGVKRIALVSDEPDKYPSRDTFAPITSFHHRRELDAVQRELREFKGVSVIIYDQT 606
            +    EGV+RIALVSD+  K+  R  F   T+FH R E+D++QRELR+  GV+V+IY+QT
Sbjct: 549  QTCRAEGVERIALVSDDITKF-GRAEFPAGTTFHDRAEMDSLQRELRDIPGVTVLIYEQT 607

Query: 607  CATEKRRRRKRGKMEDPAKRAFINPAVCEGCGDCGEKSNCLAVLPLETELGRKREIDQNA 666
            CATEKRRRRKRG MEDP K  +IN  VCEGCGDC   SNCL+V P ET LGRKR+I+ ++
Sbjct: 608  CATEKRRRRKRGMMEDPQKFVWINDLVCEGCGDCSVASNCLSVEPRETPLGRKRKINLSS 667

Query: 667  CNKDFSCVEGFCPSFVTVHGGGLRKPEAVAGGIEA--ATLPEPQHPTLDRPWNVLIPGVG 724
            CNKDFSC+ GFCPSFVT+ G   RK ++V   ++A  A LP P   +L  P+++L+ GVG
Sbjct: 668  CNKDFSCLNGFCPSFVTIEGATRRK-QSVDLDLDALEAGLPLPSAASLGSPFDLLVTGVG 726

Query: 725  GSGVTTLGALLGMAAHLEGKGCTVLDQAGLAQKFGPVTTHVRIAAKQSDIYAVRIAAGEA 784
            G+GV T+GAL+ MAAHLEGKG +VLD  G AQKFG V +++R+  +   +  VRI  G A
Sbjct: 727  GTGVVTVGALITMAAHLEGKGASVLDFTGFAQKFGTVLSYIRLGKEPDTLNQVRIDQGAA 786

Query: 785  DLLLGCDLIVAAGDESLTRLNEQISNAVVNSHESATAEFTRNPDAQVPGAAMRQAISDAV 844
            D ++GCD++V++  ++        +  V+N  E  T +   + DAQ+   A  QAI+D V
Sbjct: 787  DAVIGCDVVVSSAPKASAHYAPG-TRVVLNRAEMPTGDLVLHRDAQLRVDAREQAIADVV 845

Query: 845  GADKTHFVDATRLATRLLGDSIATNLFLLGFAYQQGLLPISAEAIEKAIELNGVSAKLNL 904
            GA+    +DA  +A  LLG ++  N+ +LG+A+Q+ L+P+S  A+ +AI LNGV+ K N 
Sbjct: 846  GAENLTSLDANAMAEALLGGTVFANVIMLGYAWQKALVPVSHTALSQAILLNGVAVKKNR 905

Query: 905  QAFRWGRRAVLEREAVEQLARPVDMVEPICKTLEEIVDWRVDFLTRYQSAGLARRYRQLV 964
             AF  GR   ++ E V+ LA+P +  +    TL+++++ RV FLT YQ A  A RY Q +
Sbjct: 906  LAFALGRCLAVDPERVQGLAQPTETED----TLDQLIERRVAFLTDYQDAEYANRYAQRI 961

Query: 965  ERVRDADSADDLALSKAVARYYFKLLAYKDEYEVARLYSEPEFRQQLEAQFEGDYKLQFH 1024
            + +R + S     L + +AR  F+ +AYKDE+EVARL + P+F  +L  QFEGDYK ++H
Sbjct: 962  KALRSSKSDISDRLVETIARNLFRFMAYKDEFEVARLQTSPDFSAELSQQFEGDYKTKYH 1021

Query: 1025 LAPAWLAKRDPVTGEPRKRELGPWVLNLFGVLAKFRFLRGTPLDPFGYGHDRRVERQLIS 1084
             AP  L+ R      P K  LG W+  +   L++ R LRG+PL+PFGY  + R+ R +++
Sbjct: 1022 FAPPLLSWRKDERRRPVKIALGAWMHPVLRGLSRLRGLRGSPLNPFGYHAEARLHRNILN 1081

Query: 1085 EYEKTVDELLAQLKPTNYRTAVAIAAL--PEQIRGYGPVKERSIAKARQQ 1132
             +E+ ++  + Q  PT    A  + A    +QIRG+GPV+E S   AR +
Sbjct: 1082 WFEELLN--MYQTNPTARSEAEWLRAFSAADQIRGFGPVREESFETARAE 1129


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: 2855
Number of extensions: 111
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: 1131
Length adjustment: 46
Effective length of query: 1110
Effective length of database: 1085
Effective search space:  1204350
Effective search space used:  1204350
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