Alignments for a candidate for ofo in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for ofo in Acidovorax sp. GW101-3H11

Align 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) (characterized)
to candidate Ac3H11_2707 Indolepyruvate ferredoxin oxidoreductase, alpha and beta subunits

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_2707
          Length = 1161

 Score = 1265 bits (3273), Expect = 0.0
 Identities = 657/1174 (55%), Positives = 825/1174 (70%), Gaps = 30/1174 (2%)

Query: 20   VSLEDKYTLERGRVYISGTQALVRLPMLQRERDRAAGLNTAGFISGYRGSPLGALDQSLW 79
            VSL DKY L  GRVY++GTQALVRL + Q+ RD AAGLNT GF+SGYRGSPLGA+DQ LW
Sbjct: 5    VSLADKYELPAGRVYMNGTQALVRLLLAQKARDEAAGLNTEGFVSGYRGSPLGAVDQELW 64

Query: 80   KAKQHLAAHDIVFQAGLNEDLAATSVWGSQQVNMYPDARFEGVFGMWYGKGPGVDRTSDV 139
            K +  L  H + FQ GLNE+LAATSVWG+Q V++ P AR +GVF +WYGKGPGVDR+ DV
Sbjct: 65   KNRALLDKHKVRFQPGLNEELAATSVWGTQMVSLDPKARVDGVFALWYGKGPGVDRSGDV 124

Query: 140  FKHANSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKACGLPVLYPSNVQEYLDYGLH 199
            FKH N AG + HGGVL++AGDDHA KSS+L HQSEH F A  +PVL+PS V E++++GLH
Sbjct: 125  FKHGNIAGGAPHGGVLLVAGDDHACKSSSLPHQSEHAFIAAMIPVLHPSGVNEFIEFGLH 184

Query: 200  AWAMSRYSGLWVSMKCVTDVVESSASVELDPHRVEIVLPQDFILPPGGLNIRWPDPPLEQ 259
             +AMSRYSG WV  K ++D VESS+S ++DP  VEI +PQ + +P  G +IRWPDPPLEQ
Sbjct: 185  GYAMSRYSGCWVGFKVISDTVESSSSFDIDPMSVEIKIPQSYPVPADGFSIRWPDPPLEQ 244

Query: 260  EARLLDYKWYAGLAYVRANKIDRIEIDSPHARFGIMTGGKAYLDTRQALANLGLDDETCA 319
            E RL   + YA L YVR NK++R +   P AR GI T GK+YLD R+AL+ LGLD+    
Sbjct: 245  ENRLQRERLYALLEYVRLNKLNRQDWAVPDARLGICTTGKSYLDVREALSLLGLDEAAAQ 304

Query: 320  RIGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKRQIMEYALKEELYNWRDDVRPKVY 379
             +G+RL K+G VWPLE      FA+GL EILVVEEKRQ++EY +KE LYN  +  RP+V 
Sbjct: 305  ALGVRLLKIGVVWPLEPTCVVEFAQGLDEILVVEEKRQVLEYQIKEHLYN--EPHRPRVV 362

Query: 380  GKFDEKDNAGGEW-SIPQSNWLLPAHYELSPAIIARAIATRLDKF----ELPADVRARIA 434
            GK+DE     GEW  +P S  LL  + EL+PA IA  IA RL K      LP  VR  + 
Sbjct: 363  GKYDE----SGEWVQVPSSGILLSPNGELTPAGIADVIAARLVKVYGQGVLPESVRVWLE 418

Query: 435  ARIAVIEAKEKAMAVPRVAAERKPWFCSGCPHNTSTNVPEGSRALAGIGCHYMTVWMDRS 494
             +  V         VP    +R P+FCSGCPHNTST VPEGSRALAGIGCHYM++WMDR 
Sbjct: 419  RQAVVATRSPSDAPVP----QRLPYFCSGCPHNTSTQVPEGSRALAGIGCHYMSMWMDRR 474

Query: 495  TSTFSQMGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSGLLAIRASIAAGVNITYKILYN 554
            T TFSQMGGEGV WIGQAP+    HVFANLGDGTY HSG LAIRA++AAGVNITYK+L N
Sbjct: 475  TETFSQMGGEGVPWIGQAPYTDTPHVFANLGDGTYMHSGSLAIRAAVAAGVNITYKLLVN 534

Query: 555  DAVAMTGGQPIDGKLSVQDVANQVAAEGARKIVVVTDEPEKYSAAIKLPQGVEVHHRDEL 614
            DAVAMTGGQP++G  SV  +  Q+AAEG +++ +V+DEPE + A    P+ V+V HRD +
Sbjct: 535  DAVAMTGGQPVEGAPSVPQLLRQLAAEGVKELHLVSDEPEAFQALDDFPKDVKVSHRDGM 594

Query: 615  DRIQRELREVPGATILIYDQTCATEKRRRRKRGTYPDPAKRAFINDAVCEGCGDCSVKSN 674
            D +QR LR+V G ++++Y QTCA EKRRRRK+ T  DPA+R  IN+AVCEGCGDC V+SN
Sbjct: 595  DALQRALRDVKGVSVIVYAQTCAAEKRRRRKKKTLADPARRVVINEAVCEGCGDCGVQSN 654

Query: 675  CLSVEPLETELGTKRQINQSSCNKDFSCVNGFCPSFVTAEGAQVKKPERHGVSMDNLPAL 734
            C+S+ PLET LG KRQI+QS CNKDFSCV GFCPSFV  +GA+++KP+R  V+      +
Sbjct: 655  CVSILPLETPLGRKRQIDQSGCNKDFSCVRGFCPSFVVLDGAELRKPQRDRVAPPT--GM 712

Query: 735  PQPALPGLEHPYGVLVTGVGGTGVVTIGGLLGMAAHLENKGVTVLDMAGLAQKGGAVLSH 794
             +P LP L  P+ +LV GVGGTGVVTIG L+GMAAHLE KGV VLDMAGLAQKGGAV+SH
Sbjct: 713  ARPELPVLARPWNILVAGVGGTGVVTIGALMGMAAHLEGKGVLVLDMAGLAQKGGAVMSH 772

Query: 795  VQIAAHPDQLHATRIAMGEADLVIGCDAIVSAIDDVISKTQVGRTRAIVNTAQTPTAEFI 854
            V++AA P QLHA R+A G+AD+V+GCD +V+A  D ++    GRTRA++NT   PT  F 
Sbjct: 773  VRLAADPVQLHAARVARGQADVVLGCDLMVAAAGDALASMASGRTRAVLNTDVAPTGSFT 832

Query: 855  KNPKWQFPGLSAEQDVRNAVGEACDFINASGLAVALIGDAIFTNPLVLGYAWQKGWLPLS 914
            ++P WQ    +  + V +A  +  + + AS LAVAL+GDA+ TN  +LG+AWQKGW+PL 
Sbjct: 833  RDPDWQASPDAMLERVGSAAAQV-ESLEASRLAVALMGDAVATNVFLLGFAWQKGWVPLQ 891

Query: 915  LDALVRAIELNGTAVEKNKAAFDWGRHMAHDPEHVLSLTGKLRNTAEGAEVVKLPTSSGA 974
             D+L+RAIELNG AV  N+AAF WGR  A DP  V    G         E V L  S  A
Sbjct: 892  EDSLLRAIELNGAAVGMNRAAFAWGRQAALDPAAVRRAAG-----LPSDEKVMLMPSRTA 946

Query: 975  LLEKLIAHRAEHLTAYQDAAYAQTFRDTVSRVRAAESALVGNGKPLPLTEAAARNLSKLM 1034
             L  ++A R E L  YQ+A YAQ +   V RV   E A VG  +   L    A +L KLM
Sbjct: 947  SLASILADRTERLADYQNARYAQHYAAVVRRVSDVEKARVGGER---LAREVAMSLYKLM 1003

Query: 1035 AYKDEYEVARLYTDPIFLDKLRNQFEGEPGRDYQLNFWLAPPLMAKRDEKGHLVKRRFGP 1094
            AYKDEYEVARL+T   FL +L+ +FEG    D+ ++++LAPPL+A+RD +G  VK+R+G 
Sbjct: 1004 AYKDEYEVARLHTSSDFLARLQERFEG----DFTVSYYLAPPLLARRDAQGRPVKQRYGA 1059

Query: 1095 STMKLFGVLAKLKGLRGGVFDVFGKTAERRTERALIGEYRALLEELTRGLSAANHATAIT 1154
                 F +LA+L+ LRG VFD FG T ERR ERA I E+ AL+E+L + L++ N   A+ 
Sbjct: 1060 WVQTAFRLLARLRFLRGTVFDPFGWTRERREERAAIDEFEALVEDLLKDLNSNNFNEALA 1119

Query: 1155 LASLPDDIRGFGHVKDDNLAKVRTRWTALLEQFR 1188
            LA LP  +RG+GHVK       + +   LL ++R
Sbjct: 1120 LARLPQQVRGYGHVKAREHEVAQKKALELLARWR 1153


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: 3279
Number of extensions: 141
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: 1161
Length adjustment: 47
Effective length of query: 1150
Effective length of database: 1114
Effective search space:  1281100
Effective search space used:  1281100
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