Alignments for a candidate for iorAB in Dokdonella koreensis DS-123

GapMind for catabolism of small carbon sources

Alignments for a candidate for iorAB in Dokdonella koreensis DS-123

Align phenylpyruvate ferredoxin oxidoreductase (EC 1.2.7.8) (characterized)
to candidate WP_067647538.1 I596_RS10685 indolepyruvate ferredoxin oxidoreductase family protein

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



>NCBI__GCF_001632775.1:WP_067647538.1
          Length = 1189

 Score = 1097 bits (2836), Expect = 0.0
 Identities = 597/1182 (50%), Positives = 757/1182 (64%), Gaps = 50/1182 (4%)

Query: 15   DYKLSDNLTATRGRIFLTGTQALVRLVLMQRAADKARGMNTAGFISGYRGSPLGMVDQQL 74
            +Y L    T + GRI+L+G QALVRL LMQ+  D+A G+NTAGFISGYRGSPLG  D +L
Sbjct: 11   EYTLDHKYTRSEGRIYLSGVQALVRLPLMQQMRDRAAGVNTAGFISGYRGSPLGGFDLEL 70

Query: 75   WKAKKLLAASDIRFLPAINEELGGTAVLGTQRVESDPERTVEGVFAMWYGKGPGVDRAGD 134
            WKA+K L AS I F P +NE+LG T V GTQ+    P   V+GVFAMWYGKGPGVDR GD
Sbjct: 71   WKARKHLKASAIEFTPGLNEDLGATMVWGTQQTNLFPGAKVDGVFAMWYGKGPGVDRCGD 130

Query: 135  ALKHGNAYGSSPHGGVLVVAGDDHGCVSSSMPHQSDFAMMAWHMPVVNPSNIADMLEFGL 194
              KHGNA G+S HGGVL +A DDH C SS++PH S+   ++  MP++NP+ + D+L+ GL
Sbjct: 131  VFKHGNAAGTSRHGGVLALAADDHACRSSTLPHGSELEFVSAMMPILNPAGVQDILDMGL 190

Query: 195  YGWELSRFSGAWVGYKAISETVESGSTVDLDALRTDWTMPQDFEVPAGGLHNRWPDLPSL 254
             GW +SRF+G WVG+K I+ETVES ++V+++  + D  +P+DF +P GGL+ RWPD P L
Sbjct: 191  LGWAMSRFTGRWVGFKTIAETVESSASVNVNPHQLDIVLPEDFALPPGGLNIRWPD-PPL 249

Query: 255  TIESRMHA-KLDAVRHFARVNSIDKWIAPSPHANVGIVTCGKAHLDLMETLRRLDLTVAD 313
              E R+H   + A   FAR N ID+ +  SP A +GIVT GK++LD+++ L  L ++  D
Sbjct: 250  DQEMRLHRYAVQAATAFARANRIDRIVLDSPKARLGIVTTGKSYLDVLQALEYLGISERD 309

Query: 314  LEAAGVRIYKVGLSFPLEMTRIDAFVSGLSEVLVIEEKGPVIEQQIKDYLYNRTQGTRPI 373
                G+R+YK+G+++PLE   I  F  GL +V+V+EEK   IE Q+K+Y+YN    TRP 
Sbjct: 310  AREIGIRVYKIGMTWPLEPVGIRQFADGLEDVIVVEEKRSFIESQMKEYMYN--WPTRPS 367

Query: 374  VVGKNAEDGTLLLSSLGELRPSRILPVFANWLAKHKPALDRRERVVDLVA-PQILSNAAD 432
            VVGK  EDG  +L S  EL P+ I  V A  L++   +   R RV  + A  Q L+    
Sbjct: 368  VVGKYDEDGNWVLPSTNELTPAMIALVIARRLSRFFSSEAIRARVAWIEAKEQELTLPRA 427

Query: 433  SVKRTPYFCSGCPHNTSTKVPEGSIAHAGIGCHFMASWMERDTTGLIQMGGEGVDWASHS 492
            +  R  ++CSGCPHNTST VPEGS A  GIGCH+M +WM+R T     MGGEGV W   +
Sbjct: 428  NFPRAAHYCSGCPHNTSTAVPEGSRAQGGIGCHYMVTWMDRRTDTFSHMGGEGVTWCGQA 487

Query: 493  MFTKTRHVFQNLGDGTYFHSGILAIRQAVAAKATITYKILYNDAVAMTGGQPVDGSISVP 552
             FT+T HVFQNLGDGTYFHSG LAIRQA+AAK  ITYKILYNDAVAMTGGQPVDG+++VP
Sbjct: 488  PFTETEHVFQNLGDGTYFHSGSLAIRQAIAAKVNITYKILYNDAVAMTGGQPVDGTLTVP 547

Query: 553  QIARQVEAEGVSRFVVVSDEPEKYDGHHDQFPKGTTFHHRSEMDTVQRQLRDTDGVTVLI 612
             IA Q+ AEGV   +VVSD+  K+    + FP G  F HR E+D VQ+++R   GV++LI
Sbjct: 548  DIAHQMRAEGVQAIIVVSDDIAKW-SRPEIFPSGVEFVHRDELDAVQKRMRQIKGVSILI 606

Query: 613  YDQTCAAEKRRRRKKGEFPDPDKRLFINEEVCEGCGDCGVQSNCLSVEPVETALGRKRRI 672
            YDQTCA EKRRRRK+G+  DP KR+FIN  VCEGCGDCG +S C+SV P ET  GRKR I
Sbjct: 607  YDQTCATEKRRRRKRGKLEDPKKRVFINSLVCEGCGDCGAKSFCVSVLPKETEYGRKREI 666

Query: 673  DQSSCNKDYSCVNGFCPSFVTVEGGKL--KKAAGAAFDPQALAARVEALPIPATHLDAAP 730
            DQS CNKDYSCV GFCPSFVTV GG L  KK +G A D  AL      +P+ AT LD  P
Sbjct: 667  DQSGCNKDYSCVKGFCPSFVTVHGGGLRKKKGSGGAVDFGAL-----PMPVFATALD-QP 720

Query: 731  YDILVTGVGGTGVVTVGALISMAAHLEGKSASVLDFMGFAQKGGSVLSFVRFAARDEWLN 790
            ++ILVTG+GGTGVVT+GALI MAAHLEGK ++VLD  G AQKGG+V   +R A     ++
Sbjct: 721  WNILVTGIGGTGVVTIGALIGMAAHLEGKGSTVLDQTGLAQKGGAVTCHLRIAKSPADIH 780

Query: 791  QVRIDTQQADVLLACDMVVGASADALQTVRHGRTRIVVNTHAIPNATFVTNPDATLHADA 850
             VRI   +AD++L CDMVV     AL  +R GR+ +V+N++     TF T PD    A  
Sbjct: 781  AVRIAAGEADLVLGCDMVVVNDYWALSKIRAGRSNVVLNSYEAMPGTFTTKPDLVFPAQK 840

Query: 851  LLDKMRHAAGAERMSTCDAQALATRFLGDTIGANILMLGYAWQLGLVPVSFGAMMRAIEL 910
            ++D ++ A         DA  LAT  LGDTI AN+ MLGYAWQ G VP+S  A+MRAIEL
Sbjct: 841  IIDSVKLALDGRAPELVDATELATALLGDTIAANLFMLGYAWQKGWVPLSLDALMRAIEL 900

Query: 911  NNVAVQMNQLAFSIGRLAAED-------------------PAAL------------EALW 939
            N  A++MN  AF+ GRL A D                   P AL             A  
Sbjct: 901  NGAAIEMNTAAFNWGRLGAHDIGQVRAAAGIKPHLPSGAIPLALPIRPAAGAAVPSPAAA 960

Query: 940  QARHLAKQSVRVDTLDELIAHREGRLQTYGGASYVKRYRALVDAARRAETSVDAKSERVT 999
             A  L   ++ VD LDE IA R   L  Y  A+Y  RY ALV+  R AE      ++ +T
Sbjct: 961  GADALDDVALSVD-LDEAIARRRTFLTDYQNAAYAGRYAALVERVRAAEQQAAPGTKALT 1019

Query: 1000 RAVATTFYRLLAVKDEYEVARLHTDAVFREALEAQFEGVAGKDFGIKFNLAPPTLTRPEP 1059
             AVA   ++L+A KDEYEVARL+T   F + +   FEG    D+ I F+LAPP L R + 
Sbjct: 1020 EAVARYAFKLMAYKDEYEVARLYTRGDFEQRIRETFEG----DYTIHFHLAPPLLARKDA 1075

Query: 1060 GKNPVKKTFGQWMWPVLGTLAKFSSLRGTMLDPFGRTLERKMERELAGDYETTLQRALAR 1119
              +  K  +G W++     LA+   LRGT LD FG T ERKMER L  DY   ++  LA 
Sbjct: 1076 EGHLRKAEYGPWVFTAFRVLARLKGLRGTPLDLFGYTAERKMERRLIEDYFRQVEELLAG 1135

Query: 1120 LDAGNLEDVAKLADLHARVRGYGHVKLANLAGVKRGERDLAA 1161
            LD  N      +A +   +RGYGHVK  +LA   + + DL A
Sbjct: 1136 LDRDNHALAVDIASVPELIRGYGHVKERHLADAMKRQDDLLA 1177


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: 3223
Number of extensions: 125
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: 1195
Length of database: 1189
Length adjustment: 47
Effective length of query: 1148
Effective length of database: 1142
Effective search space:  1311016
Effective search space used:  1311016
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: 59 (27.3 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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