Alignments for a candidate for iorAB in Rhizorhabdus wittichii RW1

GapMind for catabolism of small carbon sources

Alignments for a candidate for iorAB in Rhizorhabdus wittichii RW1

Align phenylpyruvate ferredoxin oxidoreductase (EC 1.2.7.8) (characterized)
to candidate WP_011952018.1 SWIT_RS05980 indolepyruvate ferredoxin oxidoreductase family protein

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



>NCBI__GCF_000016765.1:WP_011952018.1
          Length = 1157

 Score = 1025 bits (2650), Expect = 0.0
 Identities = 559/1160 (48%), Positives = 736/1160 (63%), Gaps = 25/1160 (2%)

Query: 13   LEDRYLRESGRVFLTGTQALVRIPLMQAALDRKQGLNTAGLVSGYRGSPLGAVDQALWQA 72
            L+  Y  E G  F+TG QALVR+P+MQ  LDR+ GLNTAGLV+GYRGSPLGA DQ LW+A
Sbjct: 9    LDSIYGAEEGPSFMTGIQALVRLPMMQRRLDRRNGLNTAGLVTGYRGSPLGAYDQQLWKA 68

Query: 73   KDLLDENRIDFVPAINEDLAATILLGTQQVETDEDRQVEGVFGLWYGKGPGVDRAGDALK 132
               LD + I F P +NEDLAAT L G Q        + +GVFG+WYGKG GVDR GD  +
Sbjct: 69   SKYLDAHDIVFQPGLNEDLAATALWGAQMHRAFGRTRADGVFGIWYGKGNGVDRTGDVFR 128

Query: 133  HGTTYGSSPHGGVLVVAGDDHGCVSSSMPHQSDVAFMSFFMPTINPANIAEYLEFGLWGY 192
            +    G++P GGVL + GDDH   SS  PHQ+D  F S  MP I PA + E L  GL G+
Sbjct: 129  NANVLGTAPLGGVLAIGGDDHAAQSSMFPHQTDGIFQSVMMPVIQPATVGEILSLGLAGF 188

Query: 193  ALSRYSGCWVGFKAISETVESAASVEIPPA-PDFVTPDDFTAPESGLHY----RWPDLPG 247
            ALSR+SG WV  K I+E VESAAS E+P + P F++P +   P  GL++     WP    
Sbjct: 189  ALSRFSGLWVAMKTIAEVVESAASFELPDSYPRFISPAE-AVPAHGLNWDPRVAWP-AQR 246

Query: 248  PQLETR-IEHKLAAVQAFARANRIDRCLFDNKEARFGIVTTGKGHLDLLEALDLLGIDED 306
             +LE R IE +L AV A+ARAN IDR +      R  +VT GK H D+++AL  LGIDE 
Sbjct: 247  TELERRMIEERLPAVTAWARANEIDRPVLQGGGRRLCVVTVGKAHQDVMQALANLGIDEG 306

Query: 307  KARDMGLDIYKVGMVWPLERRGILDFVHGKEEVLVIEEKRGIIESQIKEYMSEPDRPG-E 365
             AR +GL +YKV M WPL+   +L F  G EE+LV+EEKR ++E Q+K  +   +R G  
Sbjct: 307  GARAIGLSVYKVAMSWPLDSASLLAFADGFEEILVVEEKRPVVEEQVKVALF--NRSGAR 364

Query: 366  VLITGKQDELGRPLIPYVGELSPKLVAGFLAARLGRFFEVDFSERMAEISA-MTTAQDPG 424
              +TGK D  GR L+P   E  P +VA  +  RL      D + R+A I A + T +   
Sbjct: 365  PRVTGKTDAEGRALLPQTLEFDPLMVARAIVGRLPG--TADLAARLAAIEARVPTGEVVP 422

Query: 425  GVKRMPYFCSGCPHNTSTKVPEGSKALAGIGCHFMA-SWMGRNTESLIQMGGEGVNWIGK 483
               R P+FCSGCPHN+STK PEGS A  GIGCH MA S     T +  QMGGEG+ W+G 
Sbjct: 423  FPARKPFFCSGCPHNSSTKTPEGSIAGGGIGCHVMAVSQPKLKTATFSQMGGEGLQWVGA 482

Query: 484  SRYTGNPHVFQNLGEGTYFHSGSMAIRQAVAAGINITYKILFNDAVAMTGGQPVDGQITV 543
            + ++   H+FQNLG+GTY HSG +AIR AVAA  NIT+KIL+NDAVAMTGGQP +G I  
Sbjct: 483  APFSETGHIFQNLGDGTYQHSGLLAIRAAVAAKANITFKILYNDAVAMTGGQPAEGAIDP 542

Query: 544  DRIAQQMAAEGVNRVVVLSDEPEKYDGHHDLFPKDVTFHDRSELDQVQRELRDIPGCTVL 603
             RI++Q+AAEGV ++ ++SD+P+++    DL  + VT   R +LD+VQR LR++PG T +
Sbjct: 543  ARISRQLAAEGVGQIHLVSDDPDRWRAAPDL-AEGVTIAHRDDLDRVQRRLREVPGVTAI 601

Query: 604  IYDQTCAAEKRRRRKRKQFPDPAKRAFINHHVCEGCGDCSVQSNCLSVVPRKTELGRKRK 663
            IY+QTCAAEKRRRRKR +FPDP KR FIN  VCEGCGDCSVQSNC++V P +T  GRKR+
Sbjct: 602  IYEQTCAAEKRRRRKRGEFPDPDKRIFINPRVCEGCGDCSVQSNCIAVEPLETGFGRKRR 661

Query: 664  IDQSSCNKDFSCVNGFCPSFVTIEGGQLRKSRGVDTGSVLTRKLADIPAPKLPEMTGSYD 723
            I+QSSCNKDFSC+ GFCPSFV +EG  LRK  G    +    + A +P P+ P   G  +
Sbjct: 662  INQSSCNKDFSCIKGFCPSFVEVEGAVLRKPDGERLKAFEASRFAALPEPERPARDGVAN 721

Query: 724  LLVGGVGGTGVVTVGQLITMAAHLESRGASVLDFMGFAQKGGTVLSYVRMAPSPDKLHQV 783
            + V G+GG GV+T+G L+  AAHL+ RGA+VLDF G AQK G V+S VR+AP    +H V
Sbjct: 722  IYVAGIGGLGVLTIGALLGTAAHLDGRGATVLDFTGLAQKNGAVVSQVRIAPPGVPIHAV 781

Query: 784  RISNGQADAVIACDLVVASSQKALSVLRPNHTRIVANEAELPTADYVLFRDADMKADKRL 843
            RI  G+ D ++  D+VVA+ Q  L  +  + + +V N+ E PTAD V  RD  +      
Sbjct: 782  RIGAGEIDVLLGTDMVVAAGQDVLRRIAADRSVLVLNDDETPTADVVTDRDFALPGAAMA 841

Query: 844  GLLKNAVGEDHFDQLDANGIAEKLMGDTVFSNVMMLGFAWQKGLLPLSEAALMKAIELNG 903
              L       H  +L A  IAE L G+ V +N ++LG AWQKGL+PL   A+  AI  NG
Sbjct: 842  DTLTRRARATH--RLRATSIAEGLFGNNVAANTLLLGHAWQKGLIPLDAEAVRGAIRANG 899

Query: 904  VAIDRNKEAFGWGRLSAVDPSAVTDLLDDSNAQVVEVKPE-PTLDELINTRHKHLVNYQN 962
             A+  N  AF WGRL+A+D + V ++     A +    P+  T+D L       L  YQ+
Sbjct: 900  AAVSLNLRAFDWGRLAAIDLALVEEM-----AGLAAPAPQTETIDALAARLAAELTAYQD 954

Query: 963  QRWADQYRDAVAGVRKAEESLGETNLLLTRAVAQQLYRFMAYKDEYEVARLFAETDFMKE 1022
             R+A ++   VA  R+A   LG        AVA+  YR MAYKDEYEVARL A+  F   
Sbjct: 955  ARYAARFAALVAAARRAAAGLGREGEDFAEAVARNAYRLMAYKDEYEVARLHADPAFAAT 1014

Query: 1023 VNETFEGDFKVHFHLAPPLLSGETDAQGRPKKRRFGPWMFRAFRLLAKLRGLRGTAIDPF 1082
            + E F    ++  +LAPPLLS    A GRP+KRRFGPW+F AFRLLA+++GLRG+  DPF
Sbjct: 1015 LGEQFSDRRRLSVYLAPPLLSRIDPATGRPRKRRFGPWIFTAFRLLARMKGLRGSWADPF 1074

Query: 1083 RYSADRKLDRAMLKDYQSLVDRIGRELNASNYETFLQLAELPADVRGYGPVREQAAESIR 1142
             +S +R+ +R +++DY +LV  +  +L+ +      +LA LP  +RGYGPV+  A     
Sbjct: 1075 GHSHERRTERQLIEDYVALVGELAADLSPATLPIATELARLPDAIRGYGPVKAAAIAEAE 1134

Query: 1143 EKQTQLIKAL-DTGRPTLIR 1161
             ++  L++AL ++ RP+  R
Sbjct: 1135 ARKATLLEALAESRRPSEAR 1154


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: 2930
Number of extensions: 119
Number of successful extensions: 9
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: 1157
Length adjustment: 47
Effective length of query: 1125
Effective length of database: 1110
Effective search space:  1248750
Effective search space used:  1248750
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 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