Alignments for a candidate for iorAB in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for iorAB in Stenotrophomonas chelatiphaga DSM 21508

Align phenylpyruvate ferredoxin oxidoreductase (EC 1.2.7.8) (characterized)
to candidate WP_057508963.1 ABB28_RS12705 indolepyruvate ferredoxin oxidoreductase family protein

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



>NCBI__GCF_001431535.1:WP_057508963.1
          Length = 1229

 Score = 1045 bits (2701), Expect = 0.0
 Identities = 570/1218 (46%), Positives = 765/1218 (62%), Gaps = 85/1218 (6%)

Query: 2    SADTPQLD-DYKLEDRYLRESGRVFLTGTQALVRIPLMQAALDRKQGLNTAGLVSGYRGS 60
            SAD  QLD DY L+ +Y RE+GR++L+G QALVR+PLMQ   D   G+++AG +SGYRGS
Sbjct: 12   SAD--QLDRDYTLDHKYARETGRIYLSGVQALVRLPLMQRLRDAAAGIDSAGFISGYRGS 69

Query: 61   PLGAVDQALWQAKDLLDENRIDFVPAINEDLAATILLGTQQVETDEDRQVEGVFGLWYGK 120
            PLG  D  LW+A+  L+  R+ F P +NEDL AT++ GTQQ        V+GVFG+WYGK
Sbjct: 70   PLGGFDLELWRARQHLEAARVKFTPGLNEDLGATMVWGTQQTNLFPGANVQGVFGMWYGK 129

Query: 121  GPGVDRAGDALKHGTTYGSSPHGGVLVVAGDDHGCVSSSMPHQSDVAFMSFFMPTINPAN 180
            GPGVDR GD  KH    G+S  GGVL +A DDH C SS++PH S+  F+S  MP +NPA 
Sbjct: 130  GPGVDRCGDVFKHANAAGTSRLGGVLALAADDHACRSSTLPHGSEDEFVSAMMPVLNPAG 189

Query: 181  IAEYLEFGLWGYALSRYSGCWVGFKAISETVESAASVEIPP-APDFVTPDDFTAPESGLH 239
            + + L+ G+ G+A+SRY+G W+GFK I+ETVES+ASV++ P A   V PDDF  P  GL+
Sbjct: 190  VQDILDMGVLGWAMSRYTGRWIGFKTIAETVESSASVDVDPLARRIVLPDDFEMPAGGLN 249

Query: 240  YRWPDLPGPQLETRIEHKLAAVQAFARANRIDRCLFDNKEARFGIVTTGKGHLDLLEALD 299
             RWPD P  Q      + + A QAFARAN IDR + D+  AR GIVTTGK +LD+L+AL+
Sbjct: 250  IRWPDPPLDQEMRLHRYAVTAAQAFARANGIDRTVLDSPRARLGIVTTGKSYLDVLQALE 309

Query: 300  LLGIDEDKARDMGLDIYKVGMVWPLERRGILDFVHGKEEVLVIEEKRGIIESQIKEYM-- 357
             LG+DE    D+G+ +YKVGM WPLE +GI  F  G E+++V+EEKR  IE Q+KE    
Sbjct: 310  YLGLDETACADIGIRVYKVGMTWPLEPQGIARFAQGLEDIIVVEEKRAFIERQMKEQFFN 369

Query: 358  ---SEPDRPGEVLITGKQDELGRPLIPYVGELSPKLVAGFLAARLGRFFEVD-------- 406
               S   RP    I GK DE G  ++P  GEL+P  +AG +  R+ +FF  +        
Sbjct: 370  WPASWGPRPS---IVGKYDEEGEWILPSTGELTPATIAGVIGRRIQKFFNNESIEQRLQW 426

Query: 407  FSERMAEISAMTTAQDPGGVKRMPYFCSGCPHNTSTKVPEGSKALAGIGCHFMASWMGRN 466
              E+ AE+ A+  A  P    R+P++CSGCPHNTST VPEGS+AL GIGCH+M +WM R+
Sbjct: 427  MQEKEAEL-ALPRANFP----RVPHYCSGCPHNTSTTVPEGSRALGGIGCHYMVTWMDRS 481

Query: 467  TESLIQMGGEGVNWIGKSRYTGNPHVFQNLGEGTYFHSGSMAIRQAVAAGINITYKILFN 526
            T++   MGGEGV W G++ +T  PHVFQNLG+GTYFHSGS+AIRQ+VAAG+NITYKIL+N
Sbjct: 482  TDTFTHMGGEGVTWAGQAAFTDTPHVFQNLGDGTYFHSGSLAIRQSVAAGVNITYKILYN 541

Query: 527  DAVAMTGGQPVDGQITVDRIAQQMAAEGVNRVVVLSDEPEKYDGHHDLFPKDVTFHDRSE 586
            DAVAMTGGQPVDG ++V  IA+QM AEG+  +VVLSD  EK+    D FP  V FHDRS 
Sbjct: 542  DAVAMTGGQPVDGPLSVPDIARQMRAEGIQTIVVLSDNIEKWTRQRDQFPDGVAFHDRSA 601

Query: 587  LDQVQRELRDIPGCTVLIYDQTCAAEKRRRRKRKQFPDPAKRAFINHHVCEGCGDCSVQS 646
            LD VQ+ LR++ G ++LIY+QTCA EKRRRRKR +  DPAKR  IN  VCEGCGDC  +S
Sbjct: 602  LDAVQKRLREVKGVSILIYEQTCATEKRRRRKRGKLEDPAKRVVINSLVCEGCGDCGKKS 661

Query: 647  NCLSVVPRKTELGRKRKIDQSSCNKDFSCVNGFCPSFVTIEGGQLRKSRGVDTGSVLTRK 706
             C+SV+P++TE GRKR IDQS+CNKD+SC  GFCPSFVT+ GG+ RK    D  ++L   
Sbjct: 662  FCVSVLPKETEFGRKRDIDQSNCNKDYSCTTGFCPSFVTVHGGKPRKGSKRDASTLLD-- 719

Query: 707  LADIPAPKL-PEMTGSYDLLVGGVGGTGVVTVGQLITMAAHLESRGASVLDFMGFAQKGG 765
              ++PAP +   +   +++L+ GVGGTGVVT+G L+ MA HLE +G+SVLD  G AQKGG
Sbjct: 720  --NLPAPPVRTALEQPWNILITGVGGTGVVTIGALLGMAGHLEGKGSSVLDQTGLAQKGG 777

Query: 766  TVLSYVRMAPSPDKLHQVRISNGQADAVIACDLVVASSQKALSVLRPNHTRIVANEAELP 825
             V +++R+A +P  +H VRI+ G+AD V+ CD+VV +   ALS +R   T++V N  E  
Sbjct: 778  AVTTHIRIARTPADIHAVRIAAGEADLVLGCDMVVVNDYWALSKVRAGRTQVVLNTYEAM 837

Query: 826  TADYVLFRDADMKADKRLGLLKNAVGEDHFDQLDANGIAEKLMGDTVFSNVMMLGFAWQK 885
               +    D    A   +  ++ A+G +    LDA  +A  L+GD + SN+ +LG+AWQ+
Sbjct: 838  PGSFTTRPDMQFPAADIVAGIRVALGGESPLLLDATQLATALLGDAIASNLFILGYAWQQ 897

Query: 886  GLLPLSEAALMKAIELNGVAIDRNKEAFGWGRLSAVDPSAVTDL--LDDSNAQVVEVKPE 943
            GL+PLS  ALM+AIELNG A+  N++AF WGRL+AVDP AV     L  +     E  P 
Sbjct: 898  GLVPLSFDALMRAIELNGAAVAMNQQAFAWGRLAAVDPQAVQQAAGLVRNGHTSAETTPG 957

Query: 944  P----TLDELINTRHKHLVNYQNQRWADQYR-------DAVAGVRKAEESLGET--NLLL 990
            P       E  +T        +N     + R       D VA +   +  L  +   ++ 
Sbjct: 958  PLHALPPGEWESTEWGATAAPRNSSDERELRGLPGNAGDDVAFLPLDDARLSRSLDEMIT 1017

Query: 991  TRAVAQQLYRFMAYKDEYE-----------------------VAR----LFAETDFMKEV 1023
             RA     Y+  AY D Y                        VAR    L A  D  +  
Sbjct: 1018 RRAAFLVDYQDQAYADRYRSLVDRVRRGEQDTLGGSTALTETVARYLFKLMAYKDEYEVA 1077

Query: 1024 NETFEGDF------------KVHFHLAPPLLSGETDAQGRPKKRRFGPWMFRAFRLLAKL 1071
                 GDF            ++ FHLAPPL + + DAQGR  K+ +GPWM +AF +LAKL
Sbjct: 1078 RLYTSGDFQRRLQQQFEGEYQLRFHLAPPLFA-KKDAQGRLIKKEYGPWMLKAFGVLAKL 1136

Query: 1072 RGLRGTAIDPFRYSADRKLDRAMLKDYQSLVDRIGRELNASNYETFLQLAELPADVRGYG 1131
            + LRG  +DPF  +A+R  +R ++ DY++ V  +   L+       +++A +P  +RGYG
Sbjct: 1137 KFLRGGRLDPFGRTAERVGERQLITDYEATVQLLLDGLDDHRLALAVEIASIPEHIRGYG 1196

Query: 1132 PVREQAAESIREKQTQLI 1149
             V+E   E  + ++  L+
Sbjct: 1197 HVKEAHLEKAKAREATLL 1214


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: 3238
Number of extensions: 122
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 1172
Length of database: 1229
Length adjustment: 47
Effective length of query: 1125
Effective length of database: 1182
Effective search space:  1329750
Effective search space used:  1329750
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: 59 (27.3 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 2024 update 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