Alignments for a candidate for ofo in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for ofo in Pseudomonas fluorescens GW456-L13

Align 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) (characterized)
to candidate PfGW456L13_3456 Indolepyruvate ferredoxin oxidoreductase, alpha and beta subunits

Query= reanno::Cup4G11:RR42_RS19540
         (1197 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3456
          Length = 1187

 Score = 1325 bits (3428), Expect = 0.0
 Identities = 679/1191 (57%), Positives = 854/1191 (71%), Gaps = 36/1191 (3%)

Query: 18   ANVSLEDKYTLERGRVYISGTQALVRLPMLQRERDRAAGLNTAGFISGYRGSPLGALDQS 77
            A+ SL+DKY    G+V ++G QALVRLP++QR+RD A GLNTAGFISGYRGSPLG  DQ+
Sbjct: 3    ASPSLDDKYIQHSGKVLLTGIQALVRLPLMQRQRDLANGLNTAGFISGYRGSPLGGFDQA 62

Query: 78   LWKAKQHLAAHDIVFQAGLNEDLAATSVWGSQQVNMYPDARFEGVFGMWYGKGPGVDRTS 137
            LWKA+ +L  H  VF  G+NEDLAATS+WG+QQVN++  A ++GVFGMWYGKGPGVDR  
Sbjct: 63   LWKARDYLKEHHTVFHPGMNEDLAATSIWGTQQVNIFEGATYDGVFGMWYGKGPGVDRCG 122

Query: 138  DVFKHANSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKACGLPVLYPSNVQEYLDYG 197
            DVF+HAN+AG+S+ GGVL +AGDDH A+SS+L HQ+EHIFKA  +PVL PS VQEYLDYG
Sbjct: 123  DVFRHANAAGTSQFGGVLAIAGDDHGARSSSLPHQTEHIFKAVMMPVLAPSGVQEYLDYG 182

Query: 198  LHAWAMSRYSGLWVSMKCVTDVVESSASVELDPHRVEIVLPQDFILPPGGLNIRWPDPPL 257
            +H WAMSRYSG WV++K V D VES+A V++D HRV+ ++P D  LP GGLNIRWPDPPL
Sbjct: 183  MHGWAMSRYSGCWVALKAVADTVESAAVVDIDIHRVQPIIP-DIPLPEGGLNIRWPDPPL 241

Query: 258  EQEARLLDYKWYAGLAYVRANKIDRIEIDSPHARFGIMTGGKAYLDTRQALANLGLDDET 317
             QE RLL++K YA LAY R N++DRI +DSP AR GI+T GK+YLD  QAL  LG+D+  
Sbjct: 242  AQEQRLLEHKLYAALAYARVNRLDRIVMDSPKARIGIITSGKSYLDVCQALKILGIDETL 301

Query: 318  CARIGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKRQIMEYALKEELYNWRDDVRPK 377
              +IG+R+YKVG VWPLEA G R FAEGL+EI+VVEEKR ++EY LKEELYNWR+DVRP+
Sbjct: 302  AQQIGLRVYKVGMVWPLEAEGVRQFAEGLEEIVVVEEKRHMIEYQLKEELYNWREDVRPR 361

Query: 378  VYGKFDEKDNAGGEWSIPQSNWLLPAHYELSPAIIARAIATRLDKFELPADVRARIAARI 437
            + GKFD+K    GEWS+P + WLLPA  +L+PA+IARA+A R+    L       +   +
Sbjct: 362  IVGKFDDK----GEWSLPHTGWLLPATNDLTPAMIARALAKRI----LHLHQNGPLQVSL 413

Query: 438  AVIEAKEKAMAVPRVAAERKPWFCSGCPHNTSTNVPEGSRALAGIGCHYMTVWMDRSTST 497
            AV++A+  +        ER P +CSGCPHNTST VP+GSRALAGIGCHYM  W+   T T
Sbjct: 414  AVLDAQLASKGQFSNLMERVPHYCSGCPHNTSTKVPQGSRALAGIGCHYMAAWIYPQTQT 473

Query: 498  FSQMGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSGLLAIRASIAAGVNITYKILYNDAV 557
            FSQMGGEGVAWIGQAPF   +HVFANLGDGTYFHSG+LAIRA+IAA V ITYKILYNDAV
Sbjct: 474  FSQMGGEGVAWIGQAPFTKTRHVFANLGDGTYFHSGILAIRAAIAAKVQITYKILYNDAV 533

Query: 558  AMTGGQPIDGKLSVQDVANQVAAEGARKIVVVTDEPEKYSAAIKLPQGVEVHHRDELDRI 617
            AMTGGQP+DG LSV  ++ Q+AAEG ++IVVV+D+ EKY     L  GV V  RD++D +
Sbjct: 534  AMTGGQPVDGSLSVAQISRQLAAEGVQRIVVVSDDVEKYQHIRDLADGVPVLRRDKMDEV 593

Query: 618  QRELREVPGATILIYDQTCATEKRRRRKRGTYPDPAKRAFINDAVCEGCGDCSVKSNCLS 677
            Q +LR+  G + +IYDQTCA EKRRRRKRG +PDPA+R  IN+AVCEGCGDCS KSNC+S
Sbjct: 594  QEQLRQFQGVSAIIYDQTCAAEKRRRRKRGKFPDPARRVVINEAVCEGCGDCSSKSNCMS 653

Query: 678  VEPLETELGTKRQINQSSCNKDFSCVNGFCPSFVTAEGAQVKKPERHGVSMDNLPALPQP 737
            V  +ETE G KR+I+QSSCNKDF+C+NGFCPSFVT EG  ++KP+    + +++  LP P
Sbjct: 654  VVAVETEYGRKREIDQSSCNKDFTCLNGFCPSFVTVEGGTLRKPKALASAKNDVWDLPTP 713

Query: 738  ALPGLEHPYGVLVTGVGGTGVVTIGGLLGMAAHLENKGVTVLDMAGLAQKGGAVLSHVQI 797
            A   LE PY +LVTGVGGTGVVTIG LLGMAA +E KG   LDMAG+AQKGGAV SH++I
Sbjct: 714  ATVALEEPYSILVTGVGGTGVVTIGALLGMAAFIEGKGTLNLDMAGMAQKGGAVWSHIRI 773

Query: 798  AAHPDQLHATRIAMGEADLVIGCDAIVSAIDDVISKTQVGRTRAIVNTAQTPTAEFI--- 854
            AAH +QL A RIA GE  L++GCD +VSA  + +SK + G T A++N+ +T T+ F+   
Sbjct: 774  AAHQEQLFAPRIAEGETALLLGCDLVVSANTETLSKLRHGVTHALINSEETITSAFVRTF 833

Query: 855  ----------KNPKWQFPGLSAEQDVRNAVG-EACDFINASGLAVALIGDAIFTNPLVLG 903
                      K+P   F   +  + +  AVG E  DFI+AS +A AL+GD+I TN  +LG
Sbjct: 834  AQQAETGDLLKHPDPTFQTGNMSEQIAEAVGTEHADFIDASKIATALMGDSIATNTFMLG 893

Query: 904  YAWQKGWLPLSLDALVRAIELNGTAVEKNKAAFDWGRHMAHDPEHVLSLTGKLRNTAEGA 963
            YA+QKGWLP+   AL++AIELNGTAV  N +AFDWGR  AHD   VL          E  
Sbjct: 894  YAYQKGWLPVGKAALLQAIELNGTAVPFNLSAFDWGRRSAHDLPRVL-------RKLEAG 946

Query: 964  EVVKLPTSSGALLEKLIAHRAEHLTAYQDAAYAQTFRDTVSRVRAAESALVGNGKPLPLT 1023
            +V          LE+ +A R E LTAYQ+ AYAQ +R  V +   AE+AL+  G+P  L+
Sbjct: 947  KVQSPDRLLSQSLEETLARRMEFLTAYQNYAYAQRYRYRVEQFIKAETALL--GQPGKLS 1004

Query: 1024 EAAARNLSKLMAYKDEYEVARLYTDPIFLDKLRNQFEGEPGRDYQLNFWLAPPLMAKRDE 1083
             + AR   K++A KDEYEVARL+TD  FL+K++  FEG    DY+L F LAPPL+     
Sbjct: 1005 ASVARYYFKVLAIKDEYEVARLFTDGQFLEKIQAGFEG----DYRLRFHLAPPLLNDNGS 1060

Query: 1084 KGHLVKRRFGPSTMKLFGVLAKLKGLRGGVFDVFGKTAERRTERALIGEYRALLEELTRG 1143
                 KR FGP  ++ F +LA+LK LR    D FG+T ER+ ER  +  Y  +L+E+  G
Sbjct: 1061 GREPKKRSFGPWMLQGFKLLARLKFLRNTWLDPFGRTHERKVERNWLANYEQILDEVLAG 1120

Query: 1144 LSAANHATAITLASLPDDIRGFGHVKDDNLAKVRTRWTALLEQFRHPETAQ 1194
            L+      A  L  LP+ +RG+G VK+  L   + R   LLEQ+R+  TAQ
Sbjct: 1121 LTTQKLGLAQDLVELPESVRGYGPVKERFLGHAQQRQAQLLEQWRNGNTAQ 1171


Lambda     K      H
   0.319    0.135    0.407 

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: 3324
Number of extensions: 136
Number of successful extensions: 8
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: 1197
Length of database: 1187
Length adjustment: 47
Effective length of query: 1150
Effective length of database: 1140
Effective search space:  1311000
Effective search space used:  1311000
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 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