Alignments for a candidate for ofo in Xanthobacter autotrophicus Py2

GapMind for catabolism of small carbon sources

Alignments for a candidate for ofo in Xanthobacter autotrophicus Py2

Align branched-chain ketoacid ferredoxin reductase (EC 1.2.7.7) active on 4-methyl-2-oxopentanoate, (S)-3-methyl-2-oxopentanoate, or 3-methyl-2-oxobutanoate (characterized)
to candidate WP_011996048.1 XAUT_RS01975 indolepyruvate ferredoxin oxidoreductase family protein

Query= reanno::psRCH2:GFF3452
         (1156 letters)



>NCBI__GCF_000017645.1:WP_011996048.1
          Length = 1159

 Score = 1216 bits (3147), Expect = 0.0
 Identities = 623/1145 (54%), Positives = 799/1145 (69%), Gaps = 17/1145 (1%)

Query: 1    MSLAEIRLDDKYRLATGHLYLTGTQALTRLPMLQHQRDQARGLNTGGFISGYRGSPLGGL 60
            M+L  + LDDKY L    ++++GTQAL RL ++Q +RD+  GLNT G+++GYRGSPLGGL
Sbjct: 1    MALTPVSLDDKYDLTQDRVFVSGTQALVRLALMQKERDRRAGLNTAGYVTGYRGSPLGGL 60

Query: 61   DKSLWEARDYLKQHAIHFQPGVNEELAATAVWGSQQTNLFPGAKYDGVFAMWYGKGPGVD 120
            D+    A   LK + I FQ G+NE+LAATA+WGSQQ  L    ++DGVF +WYGKGPGVD
Sbjct: 61   DQQFLRAEKILKANDIKFQSGLNEDLAATALWGSQQAELRGEGRFDGVFGLWYGKGPGVD 120

Query: 121  RAGDVFKHANAAGVSPQGGVLLLAGDDHGCKSSTLPHQSEHAFIAASIPVLNPANVQEIL 180
            R+GDVF+HAN AG S  GGVL L GDDH C+SST  HQSE  F+   IPVLNPA VQEI+
Sbjct: 121  RSGDVFRHANNAGTSRHGGVLALMGDDHTCESSTTAHQSEFHFVDVMIPVLNPAGVQEII 180

Query: 181  DYGIIGWELSRYSGCWVALKTIAENVDSSAVVEVDPLRVQTRIPEDFELPEDGVHIRWPD 240
            DYG+ GW LSR+SG WV LK + + ++S+ +V+    RV+      F +P  G++IR  D
Sbjct: 181  DYGLYGWALSRFSGAWVGLKAVKDTIESTGIVDGRLERVRIEPALGFAMPPGGLNIRLGD 240

Query: 241  PPLAQEKRLNLYKIYAARAFARANNLNRVMLDSPN-PRLGIITTGKSYLDVRQALDDLGL 299
             PLAQE+RL  +K  A   F RAN LNR +    + PR+GI T GKSYLDVR ALD+LG+
Sbjct: 241  TPLAQEERLQEFKRDAVLHFLRANRLNRFITSGGSRPRIGIATVGKSYLDVRLALDELGI 300

Query: 300  DEALCASVGLRVLKVGMSWPLEPVSVHEFAQGLDEILVVEEKRSIIEDQLTGQLYNWPVS 359
            DE     +GLR+ KV   WPLE   + EFA+GLD I+VVEEKRS+IE Q+  +LY    +
Sbjct: 301  DEVRANDLGLRIWKVACPWPLETEGLKEFARGLDLIMVVEEKRSLIEVQVREELYG--TA 358

Query: 360  KRPRVVGEFDEQGNSLLPNLSELTPAMIARVIAKRLAPIYTSDSIQARLAFLAAKEKALA 419
             +P  +G+ DE+G  L P    L P  IA  + +RL        I  R+A L   ++ LA
Sbjct: 359  NQPVCIGKKDEEGRWLFPVKGSLDPNDIAIQLGRRLLAYGNIPDIAERVAELEEAQRVLA 418

Query: 420  ARSYSTVRTPHYCSGCPHNSSTKVPEGSRASAGIGCHYMVQWMDRRTETFTQMGGEGVNW 479
            A S    R P++CSGCPHNSSTKVPEG RA AGIGCHYMVQWMDR T  FTQMGGEG NW
Sbjct: 419  ATSDVATRIPYFCSGCPHNSSTKVPEGMRAYAGIGCHYMVQWMDRETTGFTQMGGEGANW 478

Query: 480  IGQAPFTDTPHMFQNLGDGTYFHSGSLAVRAAVAAGVNVTYKILYNDAVAMTGGQPIDGE 539
            IG++ F+  PH+FQNLGDGTY HSG LA+RAA AA VNVTYKIL+NDAVAMTGGQ  DG+
Sbjct: 479  IGESSFSKRPHVFQNLGDGTYNHSGYLALRAACAAKVNVTYKILFNDAVAMTGGQKHDGD 538

Query: 540  LRVDQLSRQIFHEGVKRIALVSDEPDKYPSRDTFAPITSFHHRRELDAVQRELREFKGVS 599
            L V  ++RQ+  EGV+R+ +V+DEPDKY     +    + HHR EL++VQREL E  GV+
Sbjct: 539  LTVPVIARQVAAEGVERVVVVTDEPDKYAPNTHWPTGLTIHHRDELESVQRELAEIPGVT 598

Query: 600  VIIYDQTCATEKRRRRKRGKMEDPAKRAFINPAVCEGCGDCGEKSNCLAVLPLETELGRK 659
            V+IYDQTCA+EKRRRRKRG+  DP KR  IN  VCEGCGDCG KSNC++V PLETE GRK
Sbjct: 599  VLIYDQTCASEKRRRRKRGQYPDPDKRVLINERVCEGCGDCGVKSNCVSVQPLETEWGRK 658

Query: 660  REIDQNACNKDFSCVEGFCPSFVTVHGGGLRKPEAVAGGIEA----ATLPEPQHPTLDRP 715
            REIDQ++CNKDFSCV GFCPSFVTV G    KP+ VAG   A      LPEP HP +   
Sbjct: 659  REIDQSSCNKDFSCVNGFCPSFVTVKGA---KPKKVAGAAGAEGDWPALPEPAHPEIHGT 715

Query: 716  WNVLIPGVGGSGVTTLGALLGMAAHLEGKGCTVLDQAGLAQKFGPVTTHVRIAAKQSDIY 775
            + ++  GVGG+GV T+GA+LGMAAHLEGK C ++D AGLAQK G V +H+R+A   +DI 
Sbjct: 716  YGIIATGVGGTGVVTIGAILGMAAHLEGKACGMIDMAGLAQKGGAVYSHIRLANDPADIT 775

Query: 776  AVRIAAGEADLLLGCDLIVAAGDESLTRLNEQISNAVVNSHESATAEFTRNPDAQVPGAA 835
            A+R+ A  AD++LG DL+VA   + L  +    +  VVN+HE    +FTRN D  +P   
Sbjct: 776  AIRVPARGADVVLGGDLVVAGTKKVLAAVKPGKTIVVVNTHEVLPGDFTRNADYSLPTER 835

Query: 836  MRQAISDAVGADKTHFVDATRLATRLLGDSIATNLFLLGFAYQQGLLPISAEAIEKAIEL 895
            +++ I D  G++ THF++A+RLA  L G+++A N+F++G+AYQ G LP+SAEAIE+AIEL
Sbjct: 836  IKRTIRDLAGSEMTHFIEASRLAQALFGNALAQNIFMVGYAYQFGALPLSAEAIERAIEL 895

Query: 896  NGVSAKLNLQAFRWGRRAVLEREAVEQLARPVDMV----EPICKTLEEIVDWRVDFLTRY 951
            NG +  +N  AF WGRRA  +  AVE++A P   +      +  +L+E++  RV  LT Y
Sbjct: 896  NGEAVAMNKTAFLWGRRAAHDPAAVEKVATPKGEIASDARRLSASLDEVIARRVAELTAY 955

Query: 952  QSAGLARRYRQLVERVRDADSADDL---ALSKAVARYYFKLLAYKDEYEVARLYSEPEFR 1008
            Q A   +RY +LVE+VR A++        L++AVA+  FKL+AYKDEYEV+RLY++  FR
Sbjct: 956  QDAAYGQRYARLVEKVRAAEAQKAPGRGGLAEAVAKSLFKLMAYKDEYEVSRLYADGAFR 1015

Query: 1009 QQLEAQFEGDYKLQFHLAPAWLAKRDPVTGEPRKRELGPWVLNLFGVLAKFRFLRGTPLD 1068
             Q  A F+GD   +FHLAP  LA+ DP+TGEPRK  LGPW++  FG+LAK + LRGT  D
Sbjct: 1016 AQAAAAFDGDLTFEFHLAPPLLARHDPITGEPRKMTLGPWMMRAFGLLAKLKGLRGTVFD 1075

Query: 1069 PFGYGHDRRVERQLISEYEKTVDELLAQLKPTNYRTAVAIAALPEQIRGYGPVKERSIAK 1128
            PFGY  +RR ER LI  YEKTV+EL+A L   ++  AVA+AALPE+IRG+G VK R +A 
Sbjct: 1076 PFGYTAERRTERALIGAYEKTVEELIAGLDGASHAVAVAVAALPEKIRGFGHVKARHLAA 1135

Query: 1129 ARQQE 1133
             + +E
Sbjct: 1136 VQAEE 1140


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: 3003
Number of extensions: 103
Number of successful extensions: 6
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: 1156
Length of database: 1159
Length adjustment: 47
Effective length of query: 1109
Effective length of database: 1112
Effective search space:  1233208
Effective search space used:  1233208
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 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