Alignments for a candidate for ofo in Sedimenticola selenatireducens DSM 17993

GapMind for catabolism of small carbon sources

Alignments for a candidate for ofo in Sedimenticola selenatireducens DSM 17993

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_029132670.1 A3GO_RS0106200 indolepyruvate ferredoxin oxidoreductase

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



>NCBI__GCF_000428045.1:WP_029132670.1
          Length = 1150

 Score = 1422 bits (3681), Expect = 0.0
 Identities = 699/1140 (61%), Positives = 867/1140 (76%), Gaps = 3/1140 (0%)

Query: 1    MSLAEIRLDDKYRLATGHLYLTGTQALTRLPMLQHQRDQARGLNTGGFISGYRGSPLGGL 60
            M+LA+I+LDDKY L +G +YLTG QALTRLPMLQ +RDQ  GLNT GFISGYRGSPLGGL
Sbjct: 1    MALADIKLDDKYTLDSGRVYLTGVQALTRLPMLQQKRDQQAGLNTAGFISGYRGSPLGGL 60

Query: 61   DKSLWEARDYLKQHAIHFQPGVNEELAATAVWGSQQTNLFPGAKYDGVFAMWYGKGPGVD 120
            DK LW+A+ YL QH I FQPG+NE+LAATA+WGSQQ NLF GA+YDGVF+MWYGKGPGVD
Sbjct: 61   DKELWKAKKYLDQHRITFQPGLNEDLAATAIWGSQQVNLFQGARYDGVFSMWYGKGPGVD 120

Query: 121  RAGDVFKHANAAGVSPQGGVLLLAGDDHGCKSSTLPHQSEHAFIAASIPVLNPANVQEIL 180
            R+GDVFKHANAAG SP GGVL++AGDDH  KSSTLPHQ+E+AF+ A IPVLNPA VQEIL
Sbjct: 121  RSGDVFKHANAAGTSPHGGVLVIAGDDHNSKSSTLPHQTEYAFMDAMIPVLNPAGVQEIL 180

Query: 181  DYGIIGWELSRYSGCWVALKTIAENVDSSAVVEVDPLRVQTRIPEDFELPEDGVHIRWPD 240
            DYG IGW LSRYSGCWVALKTIAE VD+SA V VD  RV+  IP D+ LPE G++IRWP 
Sbjct: 181  DYGQIGWALSRYSGCWVALKTIAETVDTSASVSVDSERVKITIPNDYVLPEGGLNIRWPH 240

Query: 241  PPLAQEKRLNLYKIYAARAFARANNLNRVMLDSPNPRLGIITTGKSYLDVRQALDDLGLD 300
             PL QE   + +++YAA AFAR N LNR+++DSP P+LGI TTGKSYLDV QAL+DLG+ 
Sbjct: 241  TPLDQESLQHRHRLYAALAFARVNKLNRIVIDSPEPKLGIATTGKSYLDVMQALEDLGIT 300

Query: 301  EALCASVGLRVLKVGMSWPLEPVSVHEFAQGLDEILVVEEKRSIIEDQLTGQLYNWPVSK 360
                A +G+R+ K+GMSWPLE   V +FA+GLDEILVVEEKR +IE+Q+  QLYNW    
Sbjct: 301  PERAAQIGIRLYKIGMSWPLEREGVRQFAEGLDEILVVEEKRGLIENQIKEQLYNWKEEV 360

Query: 361  RPRVVGEFDEQGNSLLPNLSELTPAMIARVIAKRLAPIYTSDSIQARLAFLAAKEKALAA 420
            RP+VVG+FD     LLP+  ELTPA IARVIA R+   + S+ I+ RL FL  KE  LA 
Sbjct: 361  RPKVVGKFDTANQWLLPSAGELTPARIARVIAARIERFHQSEVIEKRLHFLQKKEAELAL 420

Query: 421  RSYSTVRTPHYCSGCPHNSSTKVPEGSRASAGIGCHYMVQWMDRRTETFTQMGGEGVNWI 480
               +  R PH+CSGCPHN+ST++PEGSRA+ GIGCHYM  WMDR T+TFTQMGGEGV WI
Sbjct: 421  PRVTLDRVPHFCSGCPHNTSTQLPEGSRATGGIGCHYMATWMDRGTDTFTQMGGEGVPWI 480

Query: 481  GQAPFTDTPHMFQNLGDGTYFHSGSLAVRAAVAAGVNVTYKILYNDAVAMTGGQPIDGEL 540
            GQAPF+DT H+F NLG+GTYFHSG LA+RAA+AA VN+TYKILYNDAVAMTGGQP+DG  
Sbjct: 481  GQAPFSDTQHIFANLGEGTYFHSGVLAIRAALAANVNITYKILYNDAVAMTGGQPVDGPF 540

Query: 541  RVDQLSRQIFHEGVKRIALVSDEPDKYPSRDTFAPITSFHHRRELDAVQRELREFKGVSV 600
             V QLS+Q+  EGVKRIALVSD PDK+  R  FAP T+F+HR +L+ +QRELR   GVSV
Sbjct: 541  SVQQLSQQLAAEGVKRIALVSDHPDKFKQRSQFAPDTTFNHRDDLEKIQRELRNTPGVSV 600

Query: 601  IIYDQTCATEKRRRRKRGKMEDPAKRAFINPAVCEGCGDCGEKSNCLAVLPLETELGRKR 660
            +IY+QTCA EKRRRRKRG +EDP  R FIN AVCE CGDC  +SNCL+V+P+ETE GRKR
Sbjct: 601  LIYEQTCAAEKRRRRKRGTLEDPKVRPFINTAVCENCGDCSTRSNCLSVIPVETEFGRKR 660

Query: 661  EIDQNACNKDFSCVEGFCPSFVTVHGGGLRKPEAVAGGIEAATLPEPQHPTLDRPWNVLI 720
             IDQ++CNKD  CVEG+CPSFVTVHGG L++      G+    LP P  P L+RP ++L+
Sbjct: 661  AIDQSSCNKDMRCVEGYCPSFVTVHGGQLKRAANQPDGLAWPDLPLPVLPELERPHSILL 720

Query: 721  PGVGGSGVTTLGALLGMAAHLEGKGCTVLDQAGLAQKFGPVTTHVRIAAKQSDIYAVRIA 780
             G+GG+GV T+GALLGMAAH++G+G TVLD  GLAQK+G V +H+RIA K  DI+A+RIA
Sbjct: 721  TGIGGTGVVTIGALLGMAAHIDGRGVTVLDMTGLAQKYGAVVSHIRIAKKPEDIHAMRIA 780

Query: 781  AGEADLLLGCDLIVAAGDESLTRLNEQISNAVVNSHESATAEFTRNPDAQVPGAAMRQAI 840
            AG+AD LL CDL VA G E++ +LN + ++AV+NSH++ T+ F +  D   P  A+   +
Sbjct: 781  AGQADTLLACDLAVATGFEAMAKLNPERTDAVINSHQTMTSGFIKQKDLTFPAQALESQL 840

Query: 841  SDAVGADKTHFVDATRLATRLLGDSIATNLFLLGFAYQQGLLPISAEAIEKAIELNGVSA 900
              A       F+DA+RLA  LLGD+I  NLF++GFA+Q+G LP+S EA++KAIELNGVS 
Sbjct: 841  --AKTTRNAQFIDASRLAESLLGDAIGANLFMVGFAWQKGYLPLSLEALKKAIELNGVSV 898

Query: 901  KLNLQAFRWGRRAVLEREAVEQLARPVDMVEPICKTLEEIVDWRVDFLTRYQSAGLARRY 960
            + NL+A  WGRRA ++ EAV+QLA P        KTL+E++  R   LT YQ A  A RY
Sbjct: 899  EDNLRALLWGRRAAVDLEAVQQLAAPDKPALEPPKTLDELIAHRSQHLTDYQDAAYAARY 958

Query: 961  RQLVERVRDADSADDL-ALSKAVARYYFKLLAYKDEYEVARLYSEPEFRQQLEAQFEGDY 1019
            R LVERVR+ + A  L  L++AVA  Y +LLAYKDEYEVARLY++P FR+Q+  QFEGD+
Sbjct: 959  RYLVERVRERERALHLNGLAEAVAENYARLLAYKDEYEVARLYNDPNFREQITNQFEGDF 1018

Query: 1020 KLQFHLAPAWLAKRDPVTGEPRKRELGPWVLNLFGVLAKFRFLRGTPLDPFGYGHDRRVE 1079
             L+FH  P  L+K D  TG   KR  GPW+L + G+L++F+ LRG+ LDPF    DR++E
Sbjct: 1019 HLEFHFDPPVLSKADAETGRHGKRRFGPWMLKIMGLLSRFKRLRGSRLDPFRNNPDRQLE 1078

Query: 1080 RQLISEYEKTVDELLAQLKPTNYRTAVAIAALPEQIRGYGPVKERSIAKARQQEKLLREQ 1139
            R+LI +YE T++ LL  L   N  TA+ +A LPE+IRG+G +K+ +  +A  +++ L  Q
Sbjct: 1079 RRLIRDYESTLETLLTHLTGDNLETAITLARLPEEIRGFGYIKQAAAEQAALRQQALLAQ 1138


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: 110
Number of successful extensions: 5
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: 1150
Length adjustment: 47
Effective length of query: 1109
Effective length of database: 1103
Effective search space:  1223227
Effective search space used:  1223227
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