Aligments for a candidate for ofo in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Aligments for a candidate for ofo in Cupriavidus basilensis 4G11

Align 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) (characterized)
to candidate RR42_RS34245 RR42_RS34245 indolepyruvate ferredoxin oxidoreductase

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



>FitnessBrowser__Cup4G11:RR42_RS34245
          Length = 1186

 Score = 1776 bits (4601), Expect = 0.0
 Identities = 886/1199 (73%), Positives = 1007/1199 (83%), Gaps = 16/1199 (1%)

Query: 1    MNAPLTPPVSDAIRRALANVSLEDKYTLERGRVYISGTQALVRLPMLQRERDRAAGLNTA 60
            MNAPL    S A + ALA+VSL+DKYTLE+GRVY+SGTQALVRLPMLQ+ RD AAGLNTA
Sbjct: 1    MNAPL----SSAQQDALASVSLDDKYTLEKGRVYLSGTQALVRLPMLQKARDLAAGLNTA 56

Query: 61   GFISGYRGSPLGALDQSLWKAKQHLAAHDIVFQAGLNEDLAATSVWGSQQVNMYPDARFE 120
            GFISGYRGSPLG +DQ+LWKAK+HLAA D+VFQ G+NEDLAAT+VWG+QQVN++PDA  +
Sbjct: 57   GFISGYRGSPLGGVDQALWKAKKHLAASDVVFQPGVNEDLAATAVWGTQQVNLFPDATRD 116

Query: 121  GVFGMWYGKGPGVDRTSDVFKHANSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKAC 180
            GVF MWYGKGPGVDR+ DV KHANSAGS++HGGVL+LAGDDHAAKSS++AHQSEH+  A 
Sbjct: 117  GVFSMWYGKGPGVDRSIDVLKHANSAGSAKHGGVLLLAGDDHAAKSSSVAHQSEHVLLAS 176

Query: 181  GLPVLYPSNVQEYLDYGLHAWAMSRYSGLWVSMKCVTDVVESSASVELDPHRVEIVLPQD 240
            G+PVLYPSNVQEYLDYGLH WAMSRYSGLWVSMKCVTDVVES+ASVE+DP RV IVLP+D
Sbjct: 177  GIPVLYPSNVQEYLDYGLHGWAMSRYSGLWVSMKCVTDVVESTASVEVDPDRVRIVLPED 236

Query: 241  FILPPGGLNIRWPDPPLEQEARLLDYKWYAGLAYVRANKIDRIEIDSPHARFGIMTGGKA 300
            F +P GGLNIRWPDPPL QEARLLD+KWYA LAY+RANK++R+ +DSP+ARFGIMT GKA
Sbjct: 237  FAMPEGGLNIRWPDPPLAQEARLLDHKWYAALAYIRANKLNRVVLDSPNARFGIMTAGKA 296

Query: 301  YLDTRQALANLGLDDETCARIGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKRQIME 360
            YLD RQAL++LGLDD+TC RIGIR++KVGCVWPL+AH AR FA GL+EILVVEEKRQI+E
Sbjct: 297  YLDVRQALSDLGLDDDTCRRIGIRVFKVGCVWPLDAHDAREFATGLEEILVVEEKRQILE 356

Query: 361  YALKEELYNWRDDVRPKVYGKFDEKDNAGGEWSIPQSNWLLPAHYELSPAIIARAIATRL 420
            YALKEELYNWRDDVRPKVYGKFDE+ N GGEWS+P+ NWLLPAHYELSPA+IA+AIATRL
Sbjct: 357  YALKEELYNWRDDVRPKVYGKFDERGNHGGEWSLPRGNWLLPAHYELSPALIAKAIATRL 416

Query: 421  DKFELPADVRARIAARIAVIEAKEKAMAVPRVAAERKPWFCSGCPHNTSTNVPEGSRALA 480
            +K +LP DVR RIAAR+A+IEAKE+  A PR++ ERKPWFCSGCPHNTST VPEGSRALA
Sbjct: 417  EKSDLPTDVRERIAARVALIEAKEREAARPRISVERKPWFCSGCPHNTSTRVPEGSRALA 476

Query: 481  GIGCHYMTVWMDRSTSTFSQMGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSGLLAIRAS 540
            GIGCHYM +WMDR+T TFSQMGGEGVAW GQ  F G+KHVF NLGDGTYFHSGLLA+RAS
Sbjct: 477  GIGCHYMAMWMDRNTDTFSQMGGEGVAWTGQMHFTGEKHVFVNLGDGTYFHSGLLAVRAS 536

Query: 541  IAAGVNITYKILYNDAVAMTGGQPIDGKLSVQDVANQVAAEGARKIVVVTDEPEKYSAAI 600
            IAA  NITYKIL+NDAVAMTGGQP+DG L+V  +A+QV AEGA KIVVVTDEPEKY    
Sbjct: 537  IAAKANITYKILFNDAVAMTGGQPVDGVLTVPQIAHQVLAEGASKIVVVTDEPEKYGDGG 596

Query: 601  KLPQGVEVHHRDELDRIQRELREVPGATILIYDQTCATEKRRRRKRGTYPDPAKRAFIND 660
             LP  V VHHRD+LD IQ +LR+  G TILIYDQTCATEKRRRRKRGT  DPAKRAFIND
Sbjct: 597  MLPASVTVHHRDQLDEIQVQLRDTAGVTILIYDQTCATEKRRRRKRGTMADPAKRAFIND 656

Query: 661  AVCEGCGDCSVKSNCLSVEPLETELGTKRQINQSSCNKDFSCVNGFCPSFVTAEGAQVKK 720
            AVCEGCGDCSVKSNCLSVEPLET LGTKR+INQSSCNKDFSCVNGFCPSFVTAEGAQV+K
Sbjct: 657  AVCEGCGDCSVKSNCLSVEPLETPLGTKRKINQSSCNKDFSCVNGFCPSFVTAEGAQVRK 716

Query: 721  PERHG--VSMDNLPALPQPALPGLEHPYGVLVTGVGGTGVVTIGGLLGMAAHLENKGVTV 778
            P   G   ++ +  ALPQPALP LE PYGVLVTGVGGTGVVTIGGLLGMAAHLE KGVTV
Sbjct: 717  PAAAGGKGALADFSALPQPALPTLERPYGVLVTGVGGTGVVTIGGLLGMAAHLEQKGVTV 776

Query: 779  LDMAGLAQKGGAVLSHVQIAAHPDQLHATRIAMGEADLVIGCDAIVSAIDDVISKTQVGR 838
            LDMAGLAQKGGAV+SHVQIA  P  LHATRIA GEA LVIGCDAIVSA  +V+SKT++  
Sbjct: 777  LDMAGLAQKGGAVISHVQIAPTPAALHATRIATGEARLVIGCDAIVSASPEVLSKTRIDV 836

Query: 839  TRAIVNTAQTPTAEFIKNPKWQFPGLSAEQDVRNAVGEACDFINASGLAVALIGDAIFTN 898
            T A +N+A TPTA+FIKNP W+FPG SAEQD+R +VG+AC FI+A+  AV L+ D+I++N
Sbjct: 837  TAAAINSADTPTADFIKNPNWKFPGASAEQDLRASVGDACAFIDANAWAVKLLADSIYSN 896

Query: 899  PLVLGYAWQKGWLPLSLDALVRAIELNGTAVEKNKAAFDWGRHMAHDPEHVLSLTGKLRN 958
            PL+LG+AWQKGW+PL  ++LVRAIELNG AVEKN  AFDWGR++AH  E   +L  +L+ 
Sbjct: 897  PLLLGFAWQKGWVPLRRESLVRAIELNGVAVEKNLLAFDWGRYLAHHGE--AALAAQLQI 954

Query: 959  TAEGAEVVKLPTSSGALLEKLIAHRAEHLTAYQDAAYAQTFRDTVSRVRAAESALVGNGK 1018
            T   A+VV +P +    L+ +I  R   LTAYQ+ AYA  +R  V  VRAAE   VG   
Sbjct: 955  TPR-AQVVAMPET----LDSVIRQREALLTAYQNPAYAARYRAAVESVRAAEKR-VGANP 1008

Query: 1019 PLPLTEAAARNLSKLMAYKDEYEVARLYTDPIFLDKLRNQFEGEPGRDYQLNFWLAPPLM 1078
             LPL EA ARNL+KLMAYKDEYEVARLY DP FLDKLR QFEGEPGRDYQL+F LAPPL+
Sbjct: 1009 RLPLAEAVARNLAKLMAYKDEYEVARLYADPAFLDKLRAQFEGEPGRDYQLSFHLAPPLL 1068

Query: 1079 AKRDEKGHLVKRRFGPSTMKLFGVLAKLKGLRGGVFDVFGKTAERRTERALIGEYRALLE 1138
            AKRD  GHLVKRRFGP+ +  F +LA+ KGLRG  FDVFGKTAERR ER LI +Y A+ E
Sbjct: 1069 AKRDSHGHLVKRRFGPAMLTAFRLLARAKGLRGTAFDVFGKTAERRAERKLIEDYIAMAE 1128

Query: 1139 ELTRGLSAANHATAITLASLPDDIRGFGHVKDDNLAKVRTRWTALLEQFRHPETAQRVA 1197
            E    L+A    TA+ LASLPDDIRGFGHVK+ N+ K   R  ALL Q+R    A RVA
Sbjct: 1129 EFGATLNADRLDTAVALASLPDDIRGFGHVKEANMEKAAARRVALLAQYR--GAAARVA 1185


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: 3478
Number of extensions: 131
Number of successful extensions: 4
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: 1186
Length adjustment: 47
Effective length of query: 1150
Effective length of database: 1139
Effective search space:  1309850
Effective search space used:  1309850
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, or view the source code.

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