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_1196 Indolepyruvate ferredoxin oxidoreductase, alpha and beta subunits

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_1196
          Length = 1191

 Score = 1465 bits (3793), Expect = 0.0
 Identities = 740/1207 (61%), Positives = 917/1207 (75%), Gaps = 37/1207 (3%)

Query: 1    MNAPLTPPVSDAIRRALANVSLEDKYTLERGRVYISGTQALVRLPMLQRERDRAAGLNTA 60
            MNAPL     +++R+AL  V+L+DKY+L+ GR ++SG QALVRLPMLQR+RD  AGLNTA
Sbjct: 1    MNAPLP----ESVRKALETVTLDDKYSLDHGRAFMSGVQALVRLPMLQRQRDAVAGLNTA 56

Query: 61   GFISGYRGSPLGALDQSLWKAKQHLAAHDIVFQAGLNEDLAATSVWGSQQVNMYPDAR-F 119
            GFISGYRGSPLG  DQ+LW AK+HLAA++IVFQ G+NE+L AT+VWG+QQ+++YP ++ F
Sbjct: 57   GFISGYRGSPLGTYDQALWAAKKHLAANNIVFQPGVNEELGATAVWGTQQLDLYPQSKKF 116

Query: 120  EGVFGMWYGKGPGVDRTSDVFKHANSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKA 179
            +GVFG+WYGKGPGVDR SDVFKHAN AG+++HGGV+ +AGDDH +KSST AHQS+HIFKA
Sbjct: 117  DGVFGIWYGKGPGVDRCSDVFKHANMAGTAKHGGVIAIAGDDHISKSSTAAHQSDHIFKA 176

Query: 180  CGLPVLYPSNVQEYLDYGLHAWAMSRYSGLWVSMKCVTDVVESSASVELDPHRVEIVLPQ 239
            CG PV +PS+VQE LD GLHA+AMSR+SG+W  MK + +VVESS+S+ +DP RV+IV+P+
Sbjct: 177  CGTPVFFPSSVQEILDMGLHAFAMSRFSGVWSGMKTIQEVVESSSSINIDPDRVKIVMPE 236

Query: 240  DFILPPGGLNIRWPDPPLEQEARLLDYKWYAGLAYVRANKIDRIEIDSPHARFGIMTGGK 299
            DF++PPGGL+IRWPD PLEQEARL+DYKWYA LAY+RANK++   I+  + RFGI+  GK
Sbjct: 237  DFVMPPGGLHIRWPDAPLEQEARLMDYKWYAALAYIRANKLNYNVIEGKNDRFGIIASGK 296

Query: 300  AYLDTRQALANLGLDDETCARIGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKRQIM 359
            AY DTRQAL +LGLDD+TC ++GIR++KV  VWPLEA   R FA+GLQEILVVEEKRQ++
Sbjct: 297  AYNDTRQALVDLGLDDDTCRQLGIRVHKVNVVWPLEATITRDFAQGLQEILVVEEKRQVI 356

Query: 360  EYALKEELYNWRDDVRPKVYGKFDEK--DNAGGEWSI--PQSNWLLPAHYELSPAIIARA 415
            EY LKEELYNWR DVRP V GKFDE   D  GGEWS+  P  NWLL A  +L+PAIIA+A
Sbjct: 357  EYQLKEELYNWRADVRPNVLGKFDEPEGDATGGEWSMPNPSQNWLLRAKADLTPAIIAKA 416

Query: 416  IATRLDKFELPADVRARIAARIAVIEAKEKAMAVPRV-AAERKPWFCSGCPHNTSTNVPE 474
            IA RL K  + +D+ AR+ +RIAVIEA E+ MA  +V   ER PWFCSGCPHNTST VPE
Sbjct: 417  IAKRLKKLGVSSDIIARMDSRIAVIEASERGMAELKVDTGERAPWFCSGCPHNTSTRVPE 476

Query: 475  GSRALAGIGCHYMTVWM-DRSTSTFSQMGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSG 533
            GSRA+AGIGCHYM  WM DR TSTF+QMGGEGV W+GQAPF  D HVFANLGDGTYFHSG
Sbjct: 477  GSRAVAGIGCHYMANWMPDRKTSTFTQMGGEGVTWVGQAPFTTDAHVFANLGDGTYFHSG 536

Query: 534  LLAIRASIAAGVNITYKILYNDAVAMTGGQPIDGK---LSVQDVANQVAAEGARKIVVVT 590
            LLAIR SIAAG +ITYK+LYNDAVAMTGGQ +  +    SV  + N + +EG  K+++VT
Sbjct: 537  LLAIRQSIAAGTSITYKVLYNDAVAMTGGQTVGERPEGHSVLQIMNSLKSEGVVKLIIVT 596

Query: 591  DEPEKYSAAIKLPQGVEVHHRDELDRIQRELREVPGATILIYDQTCATEKRRRRKRGTYP 650
            DEP+KY   + L  GV VHHRDELD +QR+ RE+ G T++IYDQTCATEKRRRRKRGT  
Sbjct: 597  DEPQKYD-GVALAAGVTVHHRDELDTLQRQFREIKGCTVIIYDQTCATEKRRRRKRGTLA 655

Query: 651  DPAKRAFINDAVCEGCGDCSVKSNCLSVEPLETELGTKRQINQSSCNKDFSCVNGFCPSF 710
             P K   IND VCEGCGDCS KSNCLSVEP+ETE G KR+INQS+CNKD+SCVNGFCPSF
Sbjct: 656  TPDKTVVINDLVCEGCGDCSTKSNCLSVEPVETEFGRKRRINQSTCNKDYSCVNGFCPSF 715

Query: 711  VTAEGAQVKKP--ERHGVSMDNLPALPQPALPGLEHPYGVLVTGVGGTGVVTIGGLLGMA 768
            VT EG ++KKP  E+ G  +  LP++P+P LP  E  +G++V GVGGTGV+TIG LLGMA
Sbjct: 716  VTVEGGKLKKPKKEKKG-DLSALPSIPEPVLPVAEAAWGIVVGGVGGTGVITIGSLLGMA 774

Query: 769  AHLENKGVTVLDMAGLAQKGGAVLSHVQIAAHPDQLHATRIAMGEADLVIGCDAIVSAID 828
            AHL+ KGV   D  GLAQKGGA  SH+QIA  P+ ++ T++   +ADLVIGCD+IV+A  
Sbjct: 775  AHLDGKGVITQDAGGLAQKGGATWSHIQIANRPEAIYTTKVDTAKADLVIGCDSIVAAHK 834

Query: 829  DVISKTQVGRTRAIVNTAQTPTAEFIKNPKWQFPGLSAEQDVRNAVGE-ACDFINASGLA 887
              ++  Q GRT   +NT  TPTA F+ NP WQFPG + +  +  AVG       +A  +A
Sbjct: 835  YTLTVMQPGRTFVALNTHSTPTAAFVTNPDWQFPGANCDSAIAAAVGAGGVGSFDAEQVA 894

Query: 888  VALIGDAIFTNPLVLGYAWQKGWLPLSLDALVRAIELNGTAVEKNKAAFDWGRHMAHDPE 947
              L+GD+I+TNPL+LGYAWQKG +PL+L +L+RA+ELNG  V+ NKAAF+WGR  AHD  
Sbjct: 895  TQLLGDSIYTNPLMLGYAWQKGRVPLTLASLMRAMELNGVQVDNNKAAFEWGRRCAHD-- 952

Query: 948  HVLSLTGKLRNTAEGAEVVKLPTSSGALLEKLIAHRAEHLTAYQDAAYAQTFRDTVSRVR 1007
              L+    L   A+  + VK P+     L ++IA R E LT YQ+AAYA  +   V +V+
Sbjct: 953  --LASVQALFQAAQVIQFVKKPS-----LTEMIAKRVEFLTGYQNAAYAAEYHAFVEKVK 1005

Query: 1008 AAESAL-VGNGKPLPLTEAAARNLSKLMAYKDEYEVARLYTDPIFLDKLRNQFEGEPGRD 1066
            A ES L VG      L+EA AR L KLMAYKDEYEVARL+TD  F DK+ N FEG    D
Sbjct: 1006 ATESRLDVGT----RLSEAVARYLFKLMAYKDEYEVARLHTDKAFTDKIVNMFEG----D 1057

Query: 1067 YQLNFWLAPPLMAKRDEKGHLVKRRFGPSTMKLFGVLAKLKGLRGGVFDVFGKTAERRTE 1126
            Y+L   LAPP+ AK+++KG LVK+ FGP     FG+LAK+KGLRG   DVFGKT ERR E
Sbjct: 1058 YKLVHHLAPPMTAKKNDKGELVKQPFGPWMRSAFGLLAKMKGLRGTALDVFGKTEERRME 1117

Query: 1127 RALIGEYRALLEELTRGLSAANHATAITLASLPDDIRGFGHVKDDNLAKVRTRWTALLEQ 1186
            RALI EYRA ++EL   L+A N A A+ +A +P++IRG+GHVK+ +L   R +W  L+ Q
Sbjct: 1118 RALIVEYRACIDELLATLNADNLALAVEIARIPEEIRGYGHVKERHLKAARPKWDGLMAQ 1177

Query: 1187 FRHPETA 1193
            +R  + A
Sbjct: 1178 WRSGKAA 1184


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: 3290
Number of extensions: 132
Number of successful extensions: 13
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: 1191
Length adjustment: 47
Effective length of query: 1150
Effective length of database: 1144
Effective search space:  1315600
Effective search space used:  1315600
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