Alignments for a candidate for iorAB in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for iorAB in Dinoroseobacter shibae DFL-12

Align phenylpyruvate ferredoxin oxidoreductase (EC 1.2.7.8) (characterized)
to candidate 3608360 Dshi_1762 pyruvate ferredoxin/flavodoxin oxidoreductase (RefSeq)

Query= reanno::Marino:GFF880
         (1172 letters)



>FitnessBrowser__Dino:3608360
          Length = 1135

 Score =  994 bits (2569), Expect = 0.0
 Identities = 543/1162 (46%), Positives = 730/1162 (62%), Gaps = 34/1162 (2%)

Query: 8    LDDYKLEDRYLRESGRVFLTGTQALVRIPLMQAALDRKQGLNTAGLVSGYRGSPLGAVDQ 67
            L D +L DRY  +   V L GTQALVR+ LMQAA DR  GLNT G V+GYRGSPLGAVDQ
Sbjct: 3    LQDIRLSDRYDLDRETVLLNGTQALVRLTLMQAARDRAAGLNTGGYVTGYRGSPLGAVDQ 62

Query: 68   ALWQAKDLLDENRIDFVPAINEDLAATILLGTQQVETDEDRQVEGVFGLWYGKGPGVDRA 127
             + +  DLL E  + F P +NEDLAAT L GTQQ E   +   +GVFG+WYGKGPGVDR+
Sbjct: 63   QMGRNLDLLREAGVIFEPGLNEDLAATALWGTQQAELRGEGSRDGVFGMWYGKGPGVDRS 122

Query: 128  GDALKHGTTYGSSPHGGVLVVAGDDHGCVSSSMPHQSDVAFMSFFMPTINPANIAEYLEF 187
            GD +KH    G+SPHGGVL V GDDH   SS+  HQS+ A +  +MP ++PA + E L++
Sbjct: 123  GDVMKHANLAGTSPHGGVLFVMGDDHTGESSTTCHQSEFALLDAYMPVLSPAGVQEILDY 182

Query: 188  GLWGYALSRYSGCWVGFKAISETVESAASVE-IPPAPDFVTPDDFTAPESGLHYRWPDLP 246
            GL+G+ALSRY+G WVG KA+ +TVE+ A V+       FVTP D+  PE GL+ R  D  
Sbjct: 183  GLFGWALSRYAGVWVGLKAMKDTVEATAVVDGRADRMRFVTP-DYAMPEGGLNIRLVDHW 241

Query: 247  GPQLETRIEHKLAAVQAFARANRIDRCLFDNKEARFGIVTTGKGHLDLLEALDLLGIDED 306
             PQ E  I HK  A +AF  AN ID+ +     A+ G +  GK  LDL  ALDLLGID  
Sbjct: 242  TPQEERLIAHKRYAAEAFGHANGIDKRMLGKPGAKIGFLAAGKNWLDLAHALDLLGIDGA 301

Query: 307  KARDMGLDIYKVGMVWPLERRGILDFVHGKEEVLVIEEKRGIIESQIKEYMSEPDRPGEV 366
            +A  +G+  YKVGM WPL+ +G L +  G + ++V+EEKR ++E Q+KE +   DR G  
Sbjct: 302  RAEALGITAYKVGMTWPLDVKGFLGWAEGLDVIVVVEEKRKLLEVQVKEAIFN-DRRGR- 359

Query: 367  LITGKQDELGRPLIPYVGELSPKLVA---GFLAARLGRFFEVDFSERMAEISAMTTAQDP 423
             + G Q   G  L P  G L P  +A   G +    GR  E D   R+A ++ +  A + 
Sbjct: 360  RVYGGQKAPGEVLFPAYGALDPVTIAEKLGQILIEEGRASE-DLEARLARLAEVRRADNA 418

Query: 424  GGV-KRMPYFCSGCPHNTSTKVPEGSKALAGIGCHFMASWMGRNTESLIQMGGEGVNWIG 482
              +  R PYFCSGCPHNTST+VPEG+ A AGIGCH MA WM R+T     MG EG NWIG
Sbjct: 419  KDLAARTPYFCSGCPHNTSTRVPEGAIAYAGIGCHVMAMWMDRDTNGYTHMGAEGANWIG 478

Query: 483  KSRYTGNPHVFQNLGEGTYFHSGSMAIRQAVAAGINITYKILFNDAVAMTGGQPVDGQIT 542
            + +++   HVFQNLG+GTY HSG  AIR A AA  NITYKILFNDAVAMTGGQ  DG + 
Sbjct: 479  EGKFSTRSHVFQNLGDGTYNHSGIQAIRAAHAAKANITYKILFNDAVAMTGGQTNDGGLD 538

Query: 543  VDRIAQQMAAEGVNRVVVLSDEPEKYDGHHDLFPKDVTFHDRSELDQVQRELRDIPGCTV 602
              RIA ++   G+  + ++ DE E+ D     FP D+  H R EL  VQ EL+ + G T 
Sbjct: 539  AARIAWELKGIGLRDIRIVYDEKEEVD--FSAFPPDLPRHGRDELMTVQEELQQVRGTTA 596

Query: 603  LIYDQTCAAEKRRRRKRKQFPDPAKRAFINHHVCEGCGDCSVQSNCLSVVPRKTELGRKR 662
            ++Y QTCAAEKRRRRKR  FPDP KR FIN  VCEGCGDC VQSNC+++VP +TELGRKR
Sbjct: 597  ILYIQTCAAEKRRRRKRGTFPDPDKRVFINTDVCEGCGDCGVQSNCVAIVPAETELGRKR 656

Query: 663  KIDQSSCNKDFSCVNGFCPSFVTIEGGQLRKSRGVDTGSVLTRKLADIPAPKLPEMTGSY 722
             +DQS+CNKDFSC+ GFCPSFVT+ G + RK+   +        L  +P P LP + G++
Sbjct: 657  AVDQSACNKDFSCLKGFCPSFVTVSGARPRKAATAEV------DLGHLPDPALPAIDGTH 710

Query: 723  DLLVGGVGGTGVVTVGQLITMAAHLESRGASVLDFMGFAQKGGTVLSYVRMAPSPDKLHQ 782
            +LL+ GVGG GVVT+G  + MAAHLE +G  +++  G AQKGG V  + R+A  P+ +  
Sbjct: 711  NLLITGVGGMGVVTIGATLAMAAHLEGKGVGMMEMAGLAQKGGAVQIHCRIAARPEDITA 770

Query: 783  VRISNGQADAVIACDLVVASSQKALSVLRPNHTRIVANEAELPTADYVLFRDADMKADKR 842
            VR+S G+A  VI  DLVV  + K   ++    T  V N  E+ T  +   R+  +     
Sbjct: 771  VRVSVGEAHGVIGGDLVVTGAGKIQGMMAKGRTGAVVNSHEIVTGAFTRDREFRIPGADL 830

Query: 843  LGLLKNAVGEDHFDQLDANGIAEKLMGDTVFSNVMMLGFAWQKGLLPLSEAALMKAIELN 902
               L+  +G +     DA+ +A+K++GD +FSN+++ G AWQ+GL+PL   A+ +AI+LN
Sbjct: 831  QVSLQARLGAEAVVFFDASELAQKVLGDAIFSNMVVTGAAWQRGLIPLGRDAIFQAIKLN 890

Query: 903  GVAIDRNKEAFGWGRLSAVDPSAVTDLLDDSNAQVVEVKPEPTLDELINTRHKHLVNYQN 962
            G A DRNK+AF  GR + ++P AV  +L    A  V  +P+ +L E I+ R  HL  YQ+
Sbjct: 891  GAAPDRNKQAFDLGRWAVLNPEAVAKML----AAEVTARPK-SLAEKIDFRADHLRAYQS 945

Query: 963  QRWADQYRDAVAGVRKAEESLGETNLLLTRAVAQQLYRFMAYKDEYEVARLFAETDFMKE 1022
             R A +YR AV  V         T+  L   VAQ  ++ ++YKDEYEV+RL  +T    E
Sbjct: 946  ARLAKKYRRAVEAV---------TDPDLRAVVAQNYHKLLSYKDEYEVSRLLRDTRAKAE 996

Query: 1023 VNETFEGDFKVHFHLAPPLLSGETDAQGRPKKRRFGPWMFRAFRLLAKLRGLRGTAIDPF 1082
                FEG+ ++ +HLAPPLLS      GRP+KR FG W+ +A+  LA L+ LRGT +DPF
Sbjct: 997  A--AFEGELELTYHLAPPLLS-RAGPDGRPRKRAFGSWIEKAYGPLAALKLLRGTPLDPF 1053

Query: 1083 RYSADRKLDRAMLKDYQSLVDRIGRELNASNYETFLQLAELPADVRGYGPVREQAAESIR 1142
             Y+A+R+++R +++ Y++ + R+  E+  +  E    L   P  VRG+GPV+ QA E++R
Sbjct: 1054 GYTAERRMERELIRLYEADLARVQAEMTPARAEAARALLAWPDMVRGFGPVKAQAVETMR 1113

Query: 1143 EKQTQLIKALDTGRPTLIRTQQ 1164
             ++ +L  A +     + +  +
Sbjct: 1114 ARRAELWAAFEAAEDAVAQAAE 1135


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: 3088
Number of extensions: 152
Number of successful extensions: 10
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: 1172
Length of database: 1135
Length adjustment: 47
Effective length of query: 1125
Effective length of database: 1088
Effective search space:  1224000
Effective search space used:  1224000
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 (21.7 bits)
S2: 58 (26.9 bits)

This GapMind analysis is from Sep 17 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