Alignments for a candidate for ofo in Rhodospirillum rubrum ATCC 11170

GapMind for catabolism of small carbon sources

Alignments for a candidate for ofo in Rhodospirillum rubrum ATCC 11170

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 YP_427272.1 Rru_A2185 indolepyruvate ferredoxin oxidoreductase

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



>NCBI__GCF_000013085.1:YP_427272.1
          Length = 1168

 Score = 1323 bits (3424), Expect = 0.0
 Identities = 668/1136 (58%), Positives = 836/1136 (73%), Gaps = 10/1136 (0%)

Query: 8    LDDKYRLATGHLYLTGTQALTRLPMLQHQRDQARGLNTGGFISGYRGSPLGGLDKSLWEA 67
            L+DKY L  G  Y+TGTQAL RL + Q + D+  GL+T GFISGYRGSPLGG DK LW+A
Sbjct: 21   LEDKYALTGGRAYMTGTQALVRLALAQRRSDRKAGLDTRGFISGYRGSPLGGFDKELWKA 80

Query: 68   RDYLKQHAIHFQPGVNEELAATAVWGSQQTNLFPGAKYDGVFAMWYGKGPGVDRAGDVFK 127
            R +L+   I F+PG+NE+LAATAVWGSQQ  LF GA+  GVF +WYGKGPG+DR+GDVFK
Sbjct: 81   RPWLEAEGIVFKPGINEDLAATAVWGSQQVGLFKGARQQGVFGIWYGKGPGIDRSGDVFK 140

Query: 128  HANAAGVSPQGGVLLLAGDDHGCKSSTLPHQSEHAFIAASIPVLNPANVQEILDYGIIGW 187
            HAN AG +P GGVLL+AGDDH  KSST  HQ E++F+ A IPVL+PA ++E++ +G+ G 
Sbjct: 141  HANNAGTAPLGGVLLIAGDDHAAKSSTAAHQCEYSFMDAMIPVLHPAGLEEVISFGLFGL 200

Query: 188  ELSRYSGCWVALKTIAENVDSSAVVEVDPLRVQTRIPEDFELPEDGVHIRWPDPPLAQEK 247
             LSRYSGCWVALKTIAE VDSSA V +DP      +P + + P  G+HIRWPDP L QE 
Sbjct: 201  ALSRYSGCWVALKTIAETVDSSAPVLLDPDPPAFLLPAEGQAPVGGLHIRWPDPALDQEA 260

Query: 248  RLNLYKIYAARAFARANNLNRVMLDSPNPRLGIITTGKSYLDVRQALDDLGLDEALCASV 307
            RL  +K+YAA AFAR N +++V++DSP PRLGI++ GK+YLDVRQALDDLG+D A+ A++
Sbjct: 261  RLMRHKLYAALAFARVNRIDKVVMDSPVPRLGIVSVGKAYLDVRQALDDLGIDPAMAAAI 320

Query: 308  GLRVLKVGMSWPLEPVSVHEFAQGLDEILVVEEKRSIIEDQLTGQLYNWPVSKRPRVVGE 367
            GLR+ KVGM WPLE   V  FA+GL+EILVVEEKR+++E+Q+  QLYNW    RPRVVG+
Sbjct: 321  GLRLYKVGMPWPLEREGVRAFAEGLEEILVVEEKRAVVENQIKEQLYNWREDVRPRVVGK 380

Query: 368  FDEQGNSLLPNLSELTPAMIARVIAKRLAPIYTSDSIQARLAFLAAKEKALAARSYSTVR 427
            FDE G  LLP+  ELTPAM+AR +A R+    T  SI+ RL +L  K+ ALA  +    R
Sbjct: 381  FDESGAWLLPSAGELTPAMVARALAGRIGRFVTGPSIRDRLDWLERKDAALAGPTAVLKR 440

Query: 428  TPHYCSGCPHNSSTKVPEGSRASAGIGCHYMVQWM-DRRTETFTQMGGEGVNWIGQAPFT 486
             P YC+GCPHN+ST +PEGSRA AGIGCHYMV WM +R T TF+QMGGEGV WIGQAPFT
Sbjct: 441  LPTYCAGCPHNTSTTLPEGSRALAGIGCHYMVTWMPERATATFSQMGGEGVAWIGQAPFT 500

Query: 487  DTPHMFQNLGDGTYFHSGSLAVRAAVAAGVNVTYKILYNDAVAMTGGQPIDGELRVDQLS 546
            D PH+F NLGDGTYFHSG LA+RAAVAAGVNVTYKIL NDAVAMTGGQPIDG L VD LS
Sbjct: 501  DEPHVFVNLGDGTYFHSGILAIRAAVAAGVNVTYKILVNDAVAMTGGQPIDGLLSVDGLS 560

Query: 547  RQIFHEGVKRIALVSDEPDKYPSRDTFAPITSFHHRRELDAVQRELREFKGVSVIIYDQT 606
            RQ+  EGV +I +VSDEP KYP    FA   +  HR +LDA+Q++LR + GVS I+YDQT
Sbjct: 561  RQLEGEGVGKIVVVSDEPGKYPIGTVFAAGVTIRHRDDLDAIQKDLRGWPGVSAILYDQT 620

Query: 607  CATEKRRRRKRGKMEDPAKRAFINPAVCEGCGDCGEKSNCLAVLPLETELGRKREIDQNA 666
            CA EKRRRRKRG + DP +R FIN  VCEGCGDCG+ SNC+A+ PLETE GRKR +D +A
Sbjct: 621  CAAEKRRRRKRGLLADPDRRVFINDLVCEGCGDCGKVSNCVAIEPLETEFGRKRSVDLSA 680

Query: 667  CNKDFSCVEGFCPSFVTVHGGGLRKPEAVAGGIEAATLPEPQHPTLDRPWNVLIPGVGGS 726
            CNKD+SC++GFCPSFVTV G  +R+PE V G +    LPEP+   L  P+++L+ G+GG+
Sbjct: 681  CNKDYSCLKGFCPSFVTVSGAEVRRPEGV-GEVAFPPLPEPRLADLGAPYSILVTGIGGT 739

Query: 727  GVTTLGALLGMAAHLEGKGCTVLDQAGLAQKFGPVTTHVRIAAKQSDIYAVRIAAGEADL 786
            GV T+GALLGMAAHLEGKG TVLDQ GLAQK G VTTHVRIAA Q  ++AVRIAAG A+L
Sbjct: 740  GVVTIGALLGMAAHLEGKGVTVLDQTGLAQKNGAVTTHVRIAASQEALHAVRIAAGNANL 799

Query: 787  LLGCDLIVAAGDESLTRLNEQISNAVVNSHESATAEFTRNPDAQVPGAAMRQAISDAVGA 846
            LLGCD + AAG E L +   + ++AV+N+    TA FTR+PD++ P A +R A+S     
Sbjct: 800  LLGCDALTAAGPEVLAKARPRATDAVINTRPVMTAAFTRDPDSRYPEAEVRAALS--ATT 857

Query: 847  DKTHFVDATRLATRLLGDSIATNLFLLGFAYQQGLLPISAEAIEKAIELNGVSAKLNLQA 906
             +  F+DAT +AT L+GDS+ATN F++G+A+Q+GLLP+   AIE+AI LNG +   NL+A
Sbjct: 858  RRAFFLDATTIATALMGDSLATNPFMIGYAWQKGLLPLGRAAIERAITLNGAAVAFNLEA 917

Query: 907  FRWGRRAVLEREAVEQL---ARPVDMVEPICKTLEEIVDWRVDFLTRYQSAGLARRYRQL 963
              WGRRA  + EAV  L   A          +++ E ++ R  FL  YQ+A LA RYR+L
Sbjct: 918  LLWGRRAAHDLEAVTALLDRAGGGPEHHRRSESVAETIERRATFLAAYQNAALAARYRRL 977

Query: 964  VERVRDADS---ADDLALSKAVARYYFKLLAYKDEYEVARLYSEPEFRQQLEAQFEGDYK 1020
            VE V   +        ALS+AVA+ YFKLLAYKDEYEVARLYS+  F Q L A+F G  +
Sbjct: 978  VEAVVAVEKRVRPGGEALSEAVAKAYFKLLAYKDEYEVARLYSDGRFAQALAARFSGKPR 1037

Query: 1021 LQFHLAPAWLAKRDPVTGEPRKRELGPWVLNLFGVLAKFRFLRGTPLDPFGYGHDRRVER 1080
            L  HLAP  ++ RDP TG  RKR  G W+  LF +LA+ + LRGTP DPFG   +RR++R
Sbjct: 1038 LTVHLAPPLMSPRDPTTGRLRKRAFGAWIFPLFRLLARLKGLRGTPFDPFGQTSERRLQR 1097

Query: 1081 QLISEYEKTVDELLAQLKPTNYRTAVAIAALPEQIRGYGPVKERSIAKARQQEKLL 1136
            +LI+EYE T+  +L ++ P  Y  AV IA LP ++RG+GPV   ++ KA+ +E+ L
Sbjct: 1098 RLITEYETTLGVILERVDPQGYDLAVEIAGLPLEMRGFGPVLVEAVTKAQARERTL 1153


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: 3127
Number of extensions: 109
Number of successful extensions: 6
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: 1168
Length adjustment: 47
Effective length of query: 1109
Effective length of database: 1121
Effective search space:  1243189
Effective search space used:  1243189
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