Alignments for a candidate for ofo in Sulfuritalea hydrogenivorans DSM 22779

GapMind for catabolism of small carbon sources

Alignments for a candidate for ofo in Sulfuritalea hydrogenivorans DSM 22779

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_052473540.1 SUTH_RS10720 indolepyruvate ferredoxin oxidoreductase family protein

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



>NCBI__GCF_000828635.1:WP_052473540.1
          Length = 1156

 Score = 1083 bits (2800), Expect = 0.0
 Identities = 573/1149 (49%), Positives = 757/1149 (65%), Gaps = 15/1149 (1%)

Query: 5    EIRLDDKYRLATGHLYLTGTQALTRLPMLQHQRDQARGLNTGGFISGYRGSPLGGLDKSL 64
            + RL+D      G ++LTGTQAL RLP++Q QRD A GL+T GFISGYRGSPLG  D++L
Sbjct: 13   DYRLEDALAATGGRIFLTGTQALVRLPLMQRQRDIAAGLDTAGFISGYRGSPLGAYDQAL 72

Query: 65   WEARDYLKQHAIHFQPGVNEELAATAVWGSQQTNLFPGAKYDGVFAMWYGKGPGVDRAGD 124
            W A   L    IHF P +NEE  ATAV GSQQ    P     GVFA+WYGKGPGVDRA D
Sbjct: 73   WRANAQLAAANIHFLPAINEEAGATAVLGSQQVESDPQRTVTGVFALWYGKGPGVDRAAD 132

Query: 125  VFKHANAAGVSPQGGVLLLAGDDHGCKSSTLPHQSEHAFIAASIPVLNPANVQEILDYGI 184
               H NA G SP GGVL++AGDDHGC SS++PHQS+    A  +PV+NPANV E+L++G+
Sbjct: 133  ALHHGNAYGSSPTGGVLVVAGDDHGCVSSSMPHQSDFVMQAWGMPVVNPANVAEMLEFGL 192

Query: 185  IGWELSRYSGCWVALKTIAENVDSSAVVEVDPLRVQTRIPEDFELPEDGVHIRWPDPPLA 244
             GW LSR+SG WV  K I+E ++S+  V++D +  +   PE F  P  G+H R  D P  
Sbjct: 193  YGWALSRFSGAWVGFKAISETIESAMTVDLDAIAPRFAAPEGFVAPPGGLHFRPNDNPSP 252

Query: 245  QEKRLNLYKIYAARAFARANNLNRVMLDSPNPRLGIITTGKSYLDVRQALDDLGLDEALC 304
              +     K+ A R FAR N++++++   P+  +GI+T GK++ D+ +    LGL  A  
Sbjct: 253  AIELRLAAKLDAVRHFARTNSIDKLICPGPDADIGIVTCGKAHFDLMETFRRLGLSLAEL 312

Query: 305  ASVGLRVLKVGMSWPLEPVSVHEFAQGLDEILVVEEKRSIIEDQLTGQLYNWPVSKRPRV 364
             + G+R+ KVG+S+PLE   + EF   L E+LV+EEK +++E QL  Q YN P ++RPR+
Sbjct: 313  DAQGVRIYKVGLSFPLETGRIDEFCTNLKEVLVIEEKGAVVEQQLRTQFYNRPEAERPRI 372

Query: 365  VGEFDEQGNSLLPNLSELTPAMIARVIAKRLAPIYTSDSIQARLAFLAAKEKALAARSYS 424
            +G+ D  G  LL    EL P+ I  V+A  LA    +   + R+    A    L+  + +
Sbjct: 373  IGKTDVLGKPLLAATGELRPSRIMPVVANWLAGHKPALDRRERVVDFTA-PAVLSNAADA 431

Query: 425  TVRTPHYCSGCPHNSSTKVPEGSRASAGIGCHYMVQWMDRRTETFTQMGGEGVNWIGQAP 484
              R P++CSGCPHN+ST+VP GS A+ GIGCHYM  WMDR T     MGGEG++W   + 
Sbjct: 432  VKRIPYFCSGCPHNTSTRVPAGSVAAPGIGCHYMASWMDRDTAGAIHMGGEGIDWAAHSL 491

Query: 485  FTDTPHMFQNLGDGTYFHSGSLAVRAAVAAGVNVTYKILYNDAVAMTGGQPIDGELRVDQ 544
            FT   HMFQNLGDGTYFHSG LA+R A+AA  N+TYKILYNDAVAMTGGQP DG + V +
Sbjct: 492  FTTRRHMFQNLGDGTYFHSGILAIRQAIAARANITYKILYNDAVAMTGGQPPDGSISVAR 551

Query: 545  LSRQIFHEGVKRIALVSDEPDKYPSRD-TFAPITSFHHRRELDAVQRELREFKGVSVIIY 603
            ++RQ+  EG +R+ +VSD P+KY  ++  F   TSFH R ELDAVQR+LRE  GV+V+IY
Sbjct: 552  MARQVEAEGAQRVVIVSDAPEKYRGQEGDFPKGTSFHPRAELDAVQRQLREVSGVTVLIY 611

Query: 604  DQTCATEKRRRRKRGKMEDPAKRAFINPAVCEGCGDCGEKSNCLAVLPLETELGRKREID 663
            +Q CA EKRRRRK+G+    A+R FIN  VCEGCGDCG KSNCL+VLPLET LGRKR ID
Sbjct: 612  EQVCAAEKRRRRKKGESALAARRIFINSEVCEGCGDCGRKSNCLSVLPLETPLGRKRIID 671

Query: 664  QNACNKDFSCVEGFCPSFVTVHGGGLRKPEAVAGG---IEAAT-LPEPQHPTLDRPWNVL 719
            Q ACN+D+SCV+GFCPSFV+V GG  R+  A+A     ++AAT LP P+ P  D P+++L
Sbjct: 672  QAACNQDYSCVDGFCPSFVSVIGGTPRR-GAMADREQLLQAATALPLPESPLADAPYDIL 730

Query: 720  IPGVGGSGVTTLGALLGMAAHLEGKGCTVLDQAGLAQKFGPVTTHVRIAAKQSDIYAVRI 779
            + GVGG+G+ T+GAL+ MAAHL+G   +VLD  G AQK G V + VR+AA+   +   RI
Sbjct: 731  VTGVGGTGIVTIGALITMAAHLDGHSASVLDFMGFAQKGGAVLSFVRLAARPDLLNQARI 790

Query: 780  AAGEADLLLGCDLIVAAGDESLTRLNEQISNAVVNSHESATAEFTRNPDAQVPGAAMRQA 839
               +AD++L CD +V A + +L  L+   +  VVNSHE  T  F RNPDA +  A + + 
Sbjct: 791  DTQQADMMLACDTVVGASEAALQTLSRGRTRLVVNSHEIPTDAFVRNPDADLHAAELLEK 850

Query: 840  ISDAVGADKTHFVDATRLATRLLGDSIATNLFLLGFAYQQGLLPISAEAIEKAIELNGVS 899
            +  A GA +    DA  LATRLLGD++ +N+ L+G A+QQGL+P+S  AIE+AIELNGV+
Sbjct: 851  MRFAAGAGQISICDANELATRLLGDAVGSNILLMGHAWQQGLIPVSLAAIERAIELNGVA 910

Query: 900  AKLNLQAFRWGRRAVLEREAVEQLARPVDMVEPICKTLEEIVDWRVDFLTRYQSAGLARR 959
              +NL AF  GR +  E  A++++            +   +++ R   LT YQ A  A  
Sbjct: 911  VDMNLLAFHIGRLSAAEPAALDRIGSNGAAAND--DSPGALIEARAAQLTAYQDAAYADT 968

Query: 960  YRQLVERVRDADSA-----DDLALSKAVARYYFKLLAYKDEYEVARLYSEPEFRQQLEAQ 1014
            YR+LVER   A+ A      +L L++AVA+ + +LLA KDEYEVARLY++  F + L   
Sbjct: 969  YRRLVERAMHAEQAVAGSDPELPLTRAVAKNFARLLACKDEYEVARLYTDGTFSKALAEA 1028

Query: 1015 FEGDYKLQFHLAPAWLAKRDPVTGEPRKRELGPWVLNLFGVLAKFRFLRGTPLDPFGYGH 1074
            FEGDY LQFHLAP  LA  D  +G P+KR  G W+L L  +LA+ R LRGT LD FGYG 
Sbjct: 1029 FEGDYHLQFHLAPPLLAGLD-ASGAPKKRSYGQWLLPLLKLLARARRLRGTWLDIFGYGA 1087

Query: 1075 DRRVERQLISEYEKTVDELLAQLKPTNYRTAVAIAALPEQIRGYGPVKERSIAKARQQEK 1134
            +RR+ERQL S+Y + +D +L +L        + +AALPEQIRGYG VK   I KAR +E+
Sbjct: 1088 ERRLERQLASDYARMIDGVLPRLDARTLPVLLELAALPEQIRGYGHVKRAGIEKARAREQ 1147

Query: 1135 LLREQLAKG 1143
             L   LA G
Sbjct: 1148 ELLAALAAG 1156


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: 2986
Number of extensions: 112
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: 1156
Length adjustment: 47
Effective length of query: 1109
Effective length of database: 1109
Effective search space:  1229881
Effective search space used:  1229881
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 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