Alignments for a candidate for iorAB in Sulfuritalea hydrogenivorans DSM 22779

GapMind for catabolism of small carbon sources

Alignments for a candidate for iorAB in Sulfuritalea hydrogenivorans DSM 22779

Align phenylpyruvate ferredoxin oxidoreductase (EC 1.2.7.8) (characterized)
to candidate WP_052473540.1 SUTH_RS10720 indolepyruvate ferredoxin oxidoreductase family protein

Query= reanno::BFirm:BPHYT_RS02015
         (1195 letters)



>NCBI__GCF_000828635.1:WP_052473540.1
          Length = 1156

 Score = 1482 bits (3837), Expect = 0.0
 Identities = 758/1151 (65%), Positives = 883/1151 (76%), Gaps = 12/1151 (1%)

Query: 15   DYKLSDNLTATRGRIFLTGTQALVRLVLMQRAADKARGMNTAGFISGYRGSPLGMVDQQL 74
            DY+L D L AT GRIFLTGTQALVRL LMQR  D A G++TAGFISGYRGSPLG  DQ L
Sbjct: 13   DYRLEDALAATGGRIFLTGTQALVRLPLMQRQRDIAAGLDTAGFISGYRGSPLGAYDQAL 72

Query: 75   WKAKKLLAASDIRFLPAINEELGGTAVLGTQRVESDPERTVEGVFAMWYGKGPGVDRAGD 134
            W+A   LAA++I FLPAINEE G TAVLG+Q+VESDP+RTV GVFA+WYGKGPGVDRA D
Sbjct: 73   WRANAQLAAANIHFLPAINEEAGATAVLGSQQVESDPQRTVTGVFALWYGKGPGVDRAAD 132

Query: 135  ALKHGNAYGSSPHGGVLVVAGDDHGCVSSSMPHQSDFAMMAWHMPVVNPSNIADMLEFGL 194
            AL HGNAYGSSP GGVLVVAGDDHGCVSSSMPHQSDF M AW MPVVNP+N+A+MLEFGL
Sbjct: 133  ALHHGNAYGSSPTGGVLVVAGDDHGCVSSSMPHQSDFVMQAWGMPVVNPANVAEMLEFGL 192

Query: 195  YGWELSRFSGAWVGYKAISETVESGSTVDLDALRTDWTMPQDFEVPAGGLHNRWPDLPSL 254
            YGW LSRFSGAWVG+KAISET+ES  TVDLDA+   +  P+ F  P GGLH R  D PS 
Sbjct: 193  YGWALSRFSGAWVGFKAISETIESAMTVDLDAIAPRFAAPEGFVAPPGGLHFRPNDNPSP 252

Query: 255  TIESRMHAKLDAVRHFARVNSIDKWIAPSPHANVGIVTCGKAHLDLMETLRRLDLTVADL 314
             IE R+ AKLDAVRHFAR NSIDK I P P A++GIVTCGKAH DLMET RRL L++A+L
Sbjct: 253  AIELRLAAKLDAVRHFARTNSIDKLICPGPDADIGIVTCGKAHFDLMETFRRLGLSLAEL 312

Query: 315  EAAGVRIYKVGLSFPLEMTRIDAFVSGLSEVLVIEEKGPVIEQQIKDYLYNRTQGTRPIV 374
            +A GVRIYKVGLSFPLE  RID F + L EVLVIEEKG V+EQQ++   YNR +  RP +
Sbjct: 313  DAQGVRIYKVGLSFPLETGRIDEFCTNLKEVLVIEEKGAVVEQQLRTQFYNRPEAERPRI 372

Query: 375  VGKNAEDGTLLLSSLGELRPSRILPVFANWLAKHKPALDRRERVVDLVAPQILSNAADSV 434
            +GK    G  LL++ GELRPSRI+PV ANWLA HKPALDRRERVVD  AP +LSNAAD+V
Sbjct: 373  IGKTDVLGKPLLAATGELRPSRIMPVVANWLAGHKPALDRRERVVDFTAPAVLSNAADAV 432

Query: 435  KRTPYFCSGCPHNTSTKVPEGSIAHAGIGCHFMASWMERDTTGLIQMGGEGVDWASHSMF 494
            KR PYFCSGCPHNTST+VP GS+A  GIGCH+MASWM+RDT G I MGGEG+DWA+HS+F
Sbjct: 433  KRIPYFCSGCPHNTSTRVPAGSVAAPGIGCHYMASWMDRDTAGAIHMGGEGIDWAAHSLF 492

Query: 495  TKTRHVFQNLGDGTYFHSGILAIRQAVAAKATITYKILYNDAVAMTGGQPVDGSISVPQI 554
            T  RH+FQNLGDGTYFHSGILAIRQA+AA+A ITYKILYNDAVAMTGGQP DGSISV ++
Sbjct: 493  TTRRHMFQNLGDGTYFHSGILAIRQAIAARANITYKILYNDAVAMTGGQPPDGSISVARM 552

Query: 555  ARQVEAEGVSRFVVVSDEPEKYDGHHDQFPKGTTFHHRSEMDTVQRQLRDTDGVTVLIYD 614
            ARQVEAEG  R V+VSD PEKY G    FPKGT+FH R+E+D VQRQLR+  GVTVLIY+
Sbjct: 553  ARQVEAEGAQRVVIVSDAPEKYRGQEGDFPKGTSFHPRAELDAVQRQLREVSGVTVLIYE 612

Query: 615  QTCAAEKRRRRKKGEFPDPDKRLFINEEVCEGCGDCGVQSNCLSVEPVETALGRKRRIDQ 674
            Q CAAEKRRRRKKGE     +R+FIN EVCEGCGDCG +SNCLSV P+ET LGRKR IDQ
Sbjct: 613  QVCAAEKRRRRKKGESALAARRIFINSEVCEGCGDCGRKSNCLSVLPLETPLGRKRIIDQ 672

Query: 675  SSCNKDYSCVNGFCPSFVTVEGGKLKKAAGAAFDPQALAARVEALPIPATHLDAAPYDIL 734
            ++CN+DYSCV+GFCPSFV+V GG  ++  GA  D + L     ALP+P + L  APYDIL
Sbjct: 673  AACNQDYSCVDGFCPSFVSVIGGTPRR--GAMADREQLLQAATALPLPESPLADAPYDIL 730

Query: 735  VTGVGGTGVVTVGALISMAAHLEGKSASVLDFMGFAQKGGSVLSFVRFAARDEWLNQVRI 794
            VTGVGGTG+VT+GALI+MAAHL+G SASVLDFMGFAQKGG+VLSFVR AAR + LNQ RI
Sbjct: 731  VTGVGGTGIVTIGALITMAAHLDGHSASVLDFMGFAQKGGAVLSFVRLAARPDLLNQARI 790

Query: 795  DTQQADVLLACDMVVGASADALQTVRHGRTRIVVNTHAIPNATFVTNPDATLHADALLDK 854
            DTQQAD++LACD VVGAS  ALQT+  GRTR+VVN+H IP   FV NPDA LHA  LL+K
Sbjct: 791  DTQQADMMLACDTVVGASEAALQTLSRGRTRLVVNSHEIPTDAFVRNPDADLHAAELLEK 850

Query: 855  MRHAAGAERMSTCDAQALATRFLGDTIGANILMLGYAWQLGLVPVSFGAMMRAIELNNVA 914
            MR AAGA ++S CDA  LATR LGD +G+NIL++G+AWQ GL+PVS  A+ RAIELN VA
Sbjct: 851  MRFAAGAGQISICDANELATRLLGDAVGSNILLMGHAWQQGLIPVSLAAIERAIELNGVA 910

Query: 915  VQMNQLAFSIGRLAAEDPAALEALWQARHLAKQSVRVDTLDELIAHREGRLQTYGGASYV 974
            V MN LAF IGRL+A +PAAL+ +      A      D+   LI  R  +L  Y  A+Y 
Sbjct: 911  VDMNLLAFHIGRLSAAEPAALDRIGSNGAAAND----DSPGALIEARAAQLTAYQDAAYA 966

Query: 975  KRYRALVDAARRAETSVDAKSER--VTRAVATTFYRLLAVKDEYEVARLHTDAVFREALE 1032
              YR LV+ A  AE +V        +TRAVA  F RLLA KDEYEVARL+TD  F +AL 
Sbjct: 967  DTYRRLVERAMHAEQAVAGSDPELPLTRAVAKNFARLLACKDEYEVARLYTDGTFSKALA 1026

Query: 1033 AQFEGVAGKDFGIKFNLAPPTLTRPEPGKNPVKKTFGQWMWPVLGTLAKFSSLRGTMLDP 1092
              FEG    D+ ++F+LAPP L   +    P K+++GQW+ P+L  LA+   LRGT LD 
Sbjct: 1027 EAFEG----DYHLQFHLAPPLLAGLDASGAPKKRSYGQWLLPLLKLLARARRLRGTWLDI 1082

Query: 1093 FGRTLERKMERELAGDYETTLQRALARLDAGNLEDVAKLADLHARVRGYGHVKLANLAGV 1152
            FG   ER++ER+LA DY   +   L RLDA  L  + +LA L  ++RGYGHVK A +   
Sbjct: 1083 FGYGAERRLERQLASDYARMIDGVLPRLDARTLPVLLELAALPEQIRGYGHVKRAGIEKA 1142

Query: 1153 KRGERDLAARL 1163
            +  E++L A L
Sbjct: 1143 RAREQELLAAL 1153


Lambda     K      H
   0.319    0.134    0.399 

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: 3325
Number of extensions: 114
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: 1195
Length of database: 1156
Length adjustment: 47
Effective length of query: 1148
Effective length of database: 1109
Effective search space:  1273132
Effective search space used:  1273132
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