Alignments for a candidate for ofo in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for ofo in Paraburkholderia bryophila 376MFSha3.1

Align 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) (characterized)
to candidate H281DRAFT_05562 H281DRAFT_05562 indolepyruvate ferredoxin oxidoreductase

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



>FitnessBrowser__Burk376:H281DRAFT_05562
          Length = 1163

 Score = 1118 bits (2893), Expect = 0.0
 Identities = 599/1166 (51%), Positives = 761/1166 (65%), Gaps = 35/1166 (3%)

Query: 20   VSLEDKYTLERGRVYISGTQALVRLPMLQRERDRAAGLNTAGFISGYRGSPLGALDQSLW 79
            ++L+DKY L+ G  Y++G QA+VRL + Q  RD  AGL TA FISGYRGSPLG LD +LW
Sbjct: 18   LTLDDKYVLDAGSGYMTGIQAIVRLALAQHRRDATAGLKTAAFISGYRGSPLGNLDTALW 77

Query: 80   KAKQHLAAHDIVFQAGLNEDLAATSVWGSQQVNMYPDARFEGVFGMWYGKGPGVDRTSDV 139
            +A +HL AHD+VFQ G+NEDLAAT+VWGSQQ  +    +F+GV G WYGKGPGVDR+ DV
Sbjct: 78   QAGKHLTAHDVVFQPGVNEDLAATAVWGSQQSQLAGQGKFDGVVGWWYGKGPGVDRSGDV 137

Query: 140  FKHANSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKACGLPVLYPSNVQEYLDYGLH 199
             +HAN AG++ HGG + L GDDH+ KSS++ HQSEH+   CGLP+ YP++VQE LD+G+H
Sbjct: 138  LRHANLAGTAAHGGAVALYGDDHSCKSSSIPHQSEHVMIGCGLPIFYPTSVQEVLDFGVH 197

Query: 200  AWAMSRYSGLWVSMKCVTDVVESSASVELDPHRVEIVLPQDFILPPGGLNIRWPDPPLEQ 259
            A AMSR +GLW SMK V+++VE+SASV++D  RV   +  D  +P GGLNIRWPD  L Q
Sbjct: 198  AVAMSRATGLWTSMKLVSEIVETSASVDVDARRVSPNVTFDSPVPSGGLNIRWPDRSLAQ 257

Query: 260  EARLLDYKWYAGLAYVRANKIDRIEIDSPHARFGIMTGGKAYLDTRQALANLGLDDETCA 319
            E RL  YK  A LAY RAN I+++     +AR GI   GK YLDT +AL  LG++ E   
Sbjct: 258  EERLYQYKLPAALAYARANAINQVAWPCANARIGIAASGKGYLDTVEALRILGVEGEAAR 317

Query: 320  RIGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKRQIMEYALKEELYNWRDDVRPKVY 379
            RIG+RL++VG +WPLE  G R FA GLQE++VVEEKR I+E  +K+ELY   DD+RP+V 
Sbjct: 318  RIGLRLFRVGMIWPLEPAGLRVFAAGLQELIVVEEKRPILEAQIKDELYALPDDLRPRVI 377

Query: 380  GKFDEKDNAGGEWSIPQSNWLLPAHYELSPAIIARAIATRLDKFELPADVRARIAARIAV 439
            GK     +  GEWS P+S+  L +HYEL P  IA+ +A+RL +FELP D+R +I  R+  
Sbjct: 378  GK---ATDGHGEWSTPRSDAPLISHYELQPEPIAKMLASRLLRFELPEDIRQQIEQRVQA 434

Query: 440  IEAKEKAMAVPRVAAERKPWFCSGCPHNTSTNVPEGSRALAGIGCHYMTVWMDRSTSTFS 499
            IE  E+        AERK +FCSGCPHNTST VP GSR+L GIGCH++T+ MDR T TF+
Sbjct: 435  IEHAERESRKVIDIAERKAYFCSGCPHNTSTVVPTGSRSLGGIGCHFLTLTMDRGTETFT 494

Query: 500  QMGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSGLLAIRASIAAGVNITYKILYNDAVAM 559
            QMGGEG  W+G APF  + HVF NLGDGTYFHSG +AIR ++AA VNITYKILYNDAV M
Sbjct: 495  QMGGEGANWVGTAPFTKESHVFTNLGDGTYFHSGYMAIRQAVAANVNITYKILYNDAVGM 554

Query: 560  TGGQPIDGKLSVQDVANQVAAEGARKIVVVTDEPEKYSAAIKLPQGVEVHHRDELDRIQR 619
            TGGQ +DG+LSV  +  Q+AAEG  + +VV+DEP     A  L  GV V HR ELD +QR
Sbjct: 555  TGGQHVDGQLSVGQLTRQLAAEGVGQQIVVSDEPGLIGEA-GLAPGVTVRHRSELDAVQR 613

Query: 620  ELREVPGATILIYDQTCATEKRRRRKRGTYPDPAKRAFINDAVCEGCGDCSVKSNCLSVE 679
             LR V G T LIY QTCA+EKRRRRKR  YPDP +R FIN  +CEGCGDCS KSNCLSVE
Sbjct: 614  YLRTVTGVTALIYAQTCASEKRRRRKRNEYPDPDQRVFINSEICEGCGDCSKKSNCLSVE 673

Query: 680  PLETELGTKRQINQSSCNKDFSCVNGFCPSFVTAEGAQVKKPERHGVSMDNLPALPQPAL 739
            PLET LGTKRQINQSSCNKDFSC +GFCPSFVT     VK+P       D  P  P+  +
Sbjct: 674  PLETALGTKRQINQSSCNKDFSCTDGFCPSFVTVHARDVKRPAGFAGLPDGWPVAPR--M 731

Query: 740  PGLEHPYGVLVTGVGGTGVVTIGGLLGMAAHLENKGVTVLDMAGLAQKGGAVLSHVQIAA 799
            P L+ P  ++V GVGGTGVVTIG LLG AAHLE K + V+DMAG+AQKGG V S+VQ+A 
Sbjct: 732  PALDLPLRIVVGGVGGTGVVTIGALLGTAAHLEGKAIRVMDMAGMAQKGGTVYSYVQLAL 791

Query: 800  HPDQLHATRIAMGEADLVIGCDAIVSAIDDVISKTQVGRTRAIVNTAQTPTAEFIKNPKW 859
              D + ATR+A G+ DL+IG DA+V+     +S+ +     AIVN   +PT+EFI++  W
Sbjct: 792  KDDAISATRVAAGQCDLLIGADAVVAGNGTTLSRMR-SDALAIVNEDGSPTSEFIRSRDW 850

Query: 860  QFPGLSAEQDVRNAVGEA-CDFINASGLAVALIGDAIFTNPLVLGYAWQKGWLPLSLDAL 918
              P     + +R  V       + A+ +A  ++GDAIF N ++LG AWQ G +PL+  +L
Sbjct: 851  TAPVSDLLERLRARVNTGRVIALPAAQVATRILGDAIFANLMLLGMAWQAGRIPLARASL 910

Query: 919  VRAIELNGTAVEKNKAAFDWGRHMAHDPEHVLSLTGKLRNTAEGAEVVKLPTSSGALLEK 978
             RAIELNGTAV KN  AF  G H+  +P  V S+ G   N          P S    L+ 
Sbjct: 911  ERAIELNGTAVAKNLEAFRVGCHLVTEPALVRSILGHQSNE---------PVSQ--TLDD 959

Query: 979  LIAHRAEHLTAYQDAAYAQTFRDTVSRVRAAESALVGNGKPLPLTEAAARNLSKLMAYKD 1038
            LI  RA  L  Y  ++YA  +R  +   R           P  L    A  L ++MAYKD
Sbjct: 960  LIEDRAARLKKYWKSSYANQYRRLLEPAR--------RKMPEDLMITVATQLYRVMAYKD 1011

Query: 1039 EYEVARLYTDPIFLDKLRNQFEGEPGRDYQLNFWLAPPLMAKRDEKGHLVKRRFGPSTMK 1098
            EYEVAR+     F   + + F    G   +L + LAPP +    +   + KR++G     
Sbjct: 1012 EYEVARMLVSADFRRSIDDTF----GAGVRLTYHLAPPTLGTGKD---VKKRKYGQWVQW 1064

Query: 1099 LFGVLAKLKGLRGGVFDVFGKTAERRTERALIGEYRALLEELTRGLSAANHATAI-TLAS 1157
               +L K++ LR    D FG+  ERR ER     Y + +E L    S+   A+ +  +A 
Sbjct: 1065 PMTILGKMQWLRETPLDPFGRNDERRRERDWRDLYMSFVESLGSASSSRFDASVVREMAR 1124

Query: 1158 LPDDIRGFGHVKDDNLAKVRTRWTAL 1183
            LP ++RGFGHVK   +     RWT L
Sbjct: 1125 LPAEVRGFGHVKIQAMDIASRRWTEL 1150


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: 3226
Number of extensions: 128
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: 1197
Length of database: 1163
Length adjustment: 47
Effective length of query: 1150
Effective length of database: 1116
Effective search space:  1283400
Effective search space used:  1283400
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 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