Alignments for a candidate for ofo in Azospirillum sp. B510

GapMind for catabolism of small carbon sources

Alignments for a candidate for ofo in Azospirillum sp. B510

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_012974371.1 AZL_RS09275 indolepyruvate ferredoxin oxidoreductase family protein

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



>NCBI__GCF_000010725.1:WP_012974371.1
          Length = 1172

 Score = 1367 bits (3539), Expect = 0.0
 Identities = 684/1149 (59%), Positives = 842/1149 (73%), Gaps = 16/1149 (1%)

Query: 3    LAEIRLDDKYRLATGHLYLTGTQALTRLPMLQHQRDQARGLNTGGFISGYRGSPLGGLDK 62
            LA + L+DKY L  G +YLTGTQAL RLPM+Q QRD A GLNTG FISGYRGSPLGG D+
Sbjct: 8    LANVSLEDKYALERGRVYLTGTQALVRLPMMQRQRDLAAGLNTGCFISGYRGSPLGGFDQ 67

Query: 63   SLWEARDYLKQHAIHFQPGVNEELAATAVWGSQQTNLFPGAKYDGVFAMWYGKGPGVDRA 122
            +LW AR +L+++ I FQPGVNEEL ATAVWGSQQ  +F GAKYDGVFAMWYGKGPGVDR+
Sbjct: 68   NLWNARKFLERNHIRFQPGVNEELGATAVWGSQQVGMFKGAKYDGVFAMWYGKGPGVDRS 127

Query: 123  GDVFKHANAAGVSPQGGVLLLAGDDHGCKSSTLPHQSEHAFIAASIPVLNPANVQEILDY 182
            GDVFKHANAAG S  GGVL+L GDDH CKSST PHQSEHA++ A IPVLNP+ VQEILDY
Sbjct: 128  GDVFKHANAAGTSRHGGVLVLTGDDHNCKSSTFPHQSEHAYMHAMIPVLNPSGVQEILDY 187

Query: 183  GIIGWELSRYSGCWVALKTIAENVDSSAVVEVDPLRVQTRIPEDFELPEDGVHIRWPDPP 242
            G+IGW++SR+SGCW+A+KTIAE VDSSA V +DP RV   IP DF +P  G++IRWPDPP
Sbjct: 188  GLIGWQMSRWSGCWIAMKTIAETVDSSASVHIDPQRVSPVIPADFPMPPGGLNIRWPDPP 247

Query: 243  LAQEKRLNLYKIYAARAFARANNLNRVMLDSPNPRLGIITTGKSYLDVRQALDDLGLDEA 302
            L QE RL  +K+YAA AFARAN L+RV++ SP PR GI+TTGKSYLDVRQA D+LG+ E 
Sbjct: 248  LEQEYRLMKHKLYAALAFARANRLDRVVMGSPRPRFGIVTTGKSYLDVRQAFDELGIGEE 307

Query: 303  LCASVGLRVLKVGMSWPLEPVSVHEFAQGLDEILVVEEKRSIIEDQLTGQLYNWPVSKRP 362
            + A  G+ V KVGM WPLE   V  FA+GL+EI+VVEEKR++IE+QL  QLYNW    RP
Sbjct: 308  MAADWGITVYKVGMPWPLERDGVRHFAEGLEEIVVVEEKRAVIENQLKEQLYNWHPDVRP 367

Query: 363  RVVGEFDEQGNSLLPNLSELTPAMIARVIAKRLAPIYTSDSIQARLAFLAAKEKALAARS 422
            +VVG+FDEQG  +LP+  EL+PA IA VI +RL     ++++  R+AFL A+EK   A  
Sbjct: 368  KVVGKFDEQGEWILPSAGELSPAQIAVVIGRRLQRFIDNENLARRIAFLDAQEKQ-KAHV 426

Query: 423  YSTVRTPHYCSGCPHNSSTKVPEGSRASAGIGCHYMVQWMDRRTETFTQMGGEGVNWIGQ 482
               VR P +CSGCPHNSST VP+GSRA  GIGCHYM  W+DR T+TFTQMGGEGV W+GQ
Sbjct: 427  ARVVRKPTFCSGCPHNSSTVVPQGSRALGGIGCHYMATWLDRSTDTFTQMGGEGVPWVGQ 486

Query: 483  APFTDTPHMFQNLGDGTYFHSGSLAVRAAVAAGVNVTYKILYNDAVAMTGGQPIDGELRV 542
            APFT+  H+F NLGDGTYFHSG LA+R A+AA VN+TYKIL+NDAVAMTGGQP DG L V
Sbjct: 487  APFTEEKHIFANLGDGTYFHSGVLAIRQAIAAKVNITYKILFNDAVAMTGGQPFDGTLTV 546

Query: 543  DQLSRQIFHEGVKRIALVSDEPDKYPSRDTFAPITSFHHRRELDAVQRELREFKGVSVII 602
              ++  +  EGV+RI +VSDEP+KY   +     T   HR +LD VQ+E+RE  GVSV+I
Sbjct: 547  QSIAHVLRAEGVQRITVVSDEPEKYGIGNGLPQYTGVEHRDDLDRVQKEMREVPGVSVLI 606

Query: 603  YDQTCATEKRRRRKRGKMEDPAKRAFINPAVCEGCGDCGEKSNCLAVLPLETELGRKREI 662
            YDQTCATEKRRRRKRG+M DPAKR  IN  VCEGCGDC  KS+C++V+P ETE GRKR I
Sbjct: 607  YDQTCATEKRRRRKRGRMADPAKRVVINELVCEGCGDCSTKSSCVSVIPQETEFGRKRRI 666

Query: 663  DQNACNKDFSCVEGFCPSFVTVHGGGLRKPEAVAG--GIEAATLPEPQHPTLDRPWNVLI 720
            DQ++CNKD+SC +GFCPSFVTV GG LRKP+  A     +  TLP P  P  DR W++ +
Sbjct: 667  DQSSCNKDYSCTKGFCPSFVTVEGGQLRKPKPAAANPAADGGTLPAPVLPAFDRTWSLYV 726

Query: 721  PGVGGSGVTTLGALLGMAAHLEGKGCTVLDQAGLAQKFGPVTTHVRIAAKQSDIYAVRIA 780
             GVGG+GV T+GALLGMAAH+EGKG  VLD  GLAQK G VT+H+RIA    DI++VRIA
Sbjct: 727  TGVGGTGVVTIGALLGMAAHIEGKGVGVLDMTGLAQKGGAVTSHIRIAGTPEDIHSVRIA 786

Query: 781  AGEADLLLGCDLIVAAGDESLTRLNEQISNAVVNSHESATAEFTRNPDAQVPGAAMRQAI 840
            AG AD +LGCDLIVAA  + L+++    + AV+N+H+S TA+F + PD  +P   +   I
Sbjct: 787  AGGADAVLGCDLIVAAAGDGLSKMTAGRTRAVINTHDSITADFIKKPDMVIPVRDLVGDI 846

Query: 841  SDAVGADKTHFVDATRLATRLLGDSIATNLFLLGFAYQQGLLPISAEAIEKAIELNGVSA 900
              A G       DAT LAT LLGDS+  N FL+G+A+Q+GL+P+S  +I KAIELNGV+ 
Sbjct: 847  RKACGDGNVDAFDATTLATALLGDSLFANPFLMGYAWQKGLIPLSESSILKAIELNGVAV 906

Query: 901  KLNLQAFRWGRRAVLEREAVEQLARPVDMVEPI----------CKTLEEIVDWRVDFLTR 950
             LNL AFRWGRRA ++  +VE  A+P ++ E               L+E+++ R  FL  
Sbjct: 907  ALNLDAFRWGRRAAIDLASVEAAAKPREVTEATPSLLLDQRRPSTGLDEVIERRRRFLVD 966

Query: 951  YQSAGLARRYRQLVERVRDADS---ADDLALSKAVARYYFKLLAYKDEYEVARLYSEPEF 1007
            YQ A  A RY  LV+  R  +        AL++AVAR +FKL+AYKDEYEVARLY++  F
Sbjct: 967  YQDAAYAARYHALVDWTRRTEQQKIPGSTALTEAVARAHFKLMAYKDEYEVARLYTDSGF 1026

Query: 1008 RQQLEAQFEGDYKLQFHLAPAWLAKRDPVTGEPRKRELGPWVLNLFGVLAKFRFLRGTPL 1067
             + +   FEGD+KL FH+AP  L + +   GEP+K+  GPW+L +  +LAK + LRGT L
Sbjct: 1027 VENIARLFEGDWKLTFHMAPPVLGEAEADGGEPKKKSFGPWMLPVLRLLAKGKRLRGTRL 1086

Query: 1068 DPFGYGHDRRVERQLISEYEKTVDELLAQLKPTNYRTAVAIAALPEQIRGYGPVKERSIA 1127
            DPFG   +RR ER+LI+EYE  V ELL  L       AV IAALP ++RGYGPVK R++A
Sbjct: 1087 DPFGRTAERRQERRLIAEYEAVVGELLTGLTAERLDLAVEIAALPMEMRGYGPVKARNVA 1146

Query: 1128 KARQQEKLL 1136
             A+ +E  L
Sbjct: 1147 AAKAKEARL 1155


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: 3257
Number of extensions: 115
Number of successful extensions: 5
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: 1172
Length adjustment: 47
Effective length of query: 1109
Effective length of database: 1125
Effective search space:  1247625
Effective search space used:  1247625
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.

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 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