Alignments for a candidate for ofo in Polaromonas naphthalenivorans CJ2

GapMind for catabolism of small carbon sources

Alignments for a candidate for ofo in Polaromonas naphthalenivorans CJ2

Align 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) (characterized)
to candidate WP_011803249.1 PNAP_RS19430 MFS transporter

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



>NCBI__GCF_000015505.1:WP_011803249.1
          Length = 1206

 Score = 1470 bits (3806), Expect = 0.0
 Identities = 751/1224 (61%), Positives = 931/1224 (76%), Gaps = 51/1224 (4%)

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

Query: 61   GFISGYRGSPLGALDQSLWKAKQHLAAHDIVFQAGLNEDLAATSVWGSQQVNMYPDA-RF 119
            GFISGYRGSPLG  DQ+LW A++HL A +IVF+ G+NE+L AT+VWG+QQ+++YP   +F
Sbjct: 57   GFISGYRGSPLGGYDQALWAARKHLEAQNIVFKPGVNEELGATAVWGTQQLDLYPQTNKF 116

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

Query: 180  CGLPVLYPSNVQEYLDYGLHAWAMSRYSGLWVSMKCVTDVVESSASVELDPHRVEIVLPQ 239
            CGLPV +PS+VQE LD GLHA+AMSR+SG+W  MK + +VVESS+SV +DP RV+I++P+
Sbjct: 177  CGLPVFFPSSVQEILDMGLHAFAMSRFSGVWSGMKTIQEVVESSSSVSVDPDRVKIIMPE 236

Query: 240  DFILPPGGLNIRWPDPPLEQEARLLDYKWYAGLAYVRANKIDRIEIDSPHARFGIMTGGK 299
            DF +PPGGL+IRWPD PLEQEARL+DYKWYA LAYVRANK++   I S + RFGI+  GK
Sbjct: 237  DFQMPPGGLHIRWPDAPLEQEARLMDYKWYAALAYVRANKLNYNVIASANDRFGIIASGK 296

Query: 300  AYLDTRQALANLGLDDETCARIGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKRQIM 359
            A+ DTRQALA+LGLD++TC ++GIRL+KV  VWPLEA   R FA GLQEILVVEEKRQ++
Sbjct: 297  AFNDTRQALADLGLDEDTCHQLGIRLHKVNVVWPLEATITRDFAMGLQEILVVEEKRQVI 356

Query: 360  EYALKEELYNWRDDVRPKVYGKFDEK--DNAGGEWS--IPQSNWLLPAHYELSPAIIARA 415
            EY +KEELYNWR DVRP V GKFDE   D +GGEWS   P  NWLL A  +L+PAIIA+A
Sbjct: 357  EYQIKEELYNWRADVRPNVLGKFDEPEGDESGGEWSRPNPSENWLLRAKADLTPAIIAKA 416

Query: 416  IATRLDKFELPADVRARIAARIAVIEAKEKAMAVPRV-AAERKPWFCSGCPHNTSTNVPE 474
            IA RL K  +P+D+ AR+ AR+AVI+A+E+A+   ++   ER PWFCSGCPHNTST VPE
Sbjct: 417  IAKRLTKLGVPSDIVARMQARLAVIDARERALVETKLETGERAPWFCSGCPHNTSTRVPE 476

Query: 475  GSRALAGIGCHYMTVWMDRSTSTFSQMGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSGL 534
            GSRA+AGIGCHYM  WMDRSTSTF+QMGGEGV W+GQ+ F  + H+FANLGDGTYFHSGL
Sbjct: 477  GSRAVAGIGCHYMATWMDRSTSTFTQMGGEGVPWVGQSAFTTEPHIFANLGDGTYFHSGL 536

Query: 535  LAIRASIAAGVNITYKILYNDAVAMTGGQPIDGK---LSVQDVANQVAAEGARKIVVVTD 591
            LAIR SIA+GVNITYKILYNDAVAMTGGQ +  +    SV  +A+ + AEG  ++VVVTD
Sbjct: 537  LAIRQSIASGVNITYKILYNDAVAMTGGQQVGERPEGHSVAQIAHSLRAEGVARLVVVTD 596

Query: 592  EPEKY--------SAAIK---------LPQGVEVHHRDELDRIQRELREVPGATILIYDQ 634
            EPEKY        S+A +         LP G+EV HRDELDRIQRE RE+ G TI+IYDQ
Sbjct: 597  EPEKYHGRTHTLDSSAARAGHAELINDLPPGIEVFHRDELDRIQREFRELKGTTIIIYDQ 656

Query: 635  TCATEKRRRRKRGTYPDPAKRAFINDAVCEGCGDCSVKSNCLSVEPLETELGTKRQINQS 694
            TCATEKRRRRKRGT  DPAKR  IN+ VCEGCGDCSV+SNCLSVEPLETE G KRQINQ+
Sbjct: 657  TCATEKRRRRKRGTLADPAKRVVINELVCEGCGDCSVQSNCLSVEPLETEFGRKRQINQN 716

Query: 695  SCNKDFSCVNGFCPSFVTAEGAQVKKP--ERHGVSMDNLPALPQPALPGLEHPYGVLVTG 752
            +CNKD+SC+ GFCPSFVT EG Q+KKP  E+ G  + +LPA+P P LP  E+ +G++V G
Sbjct: 717  TCNKDYSCLKGFCPSFVTVEGGQLKKPKKEKKG-DLASLPAIPDPVLPVAENAWGIVVGG 775

Query: 753  VGGTGVVTIGGLLGMAAHLENKGVTVLDMAGLAQKGGAVLSHVQIAAHPDQLHATRIAMG 812
            VGGTGV+TIG LLGMAAHLE KGV   D  GLAQKGGA  SH+QIA  P+ ++ T++   
Sbjct: 776  VGGTGVITIGQLLGMAAHLEGKGVVTQDAGGLAQKGGATWSHIQIANRPEAIYTTKVDTA 835

Query: 813  EADLVIGCDAIVSAIDDVISKTQVGRTRAIVNTAQTPTAEFIKNPKWQFPGLSAEQDVRN 872
            +ADLVIGCD IV+A    ++  Q GRT   +N+   PTA F+ NP WQFPG + E  VR+
Sbjct: 836  KADLVIGCDPIVTANAYTLATMQPGRTFVAMNSHGAPTAAFVTNPDWQFPGGNCENAVRS 895

Query: 873  AVG-EACDFINASGLAVALIGDAIFTNPLVLGYAWQKGWLPLSLDALVRAIELNGTAVEK 931
            AVG +A    +A  +AV LIGD+I+TNPL+LG+AWQKG +PLS  AL+RAIELN   V+ 
Sbjct: 896  AVGADAMASFDAEQVAVQLIGDSIYTNPLMLGFAWQKGRVPLSHAALMRAIELNNVQVDN 955

Query: 932  NKAAFDWGRHMAHDPEHVLSLTGKLRNTAEGAEVVKLPTSSGALLEKLIAHRAEHLTAYQ 991
            NKAAF+WGR  AHD    L     L   A+  + VK P+     L +++  R   LTAYQ
Sbjct: 956  NKAAFEWGRRCAHD----LLAVQSLFKAAQVIQFVKKPS-----LAEMLNKRVVFLTAYQ 1006

Query: 992  DAAYAQTFRDTVSRVRAAESALVGNGKPLPLTEAAARNLSKLMAYKDEYEVARLYTDPIF 1051
            +AAYAQT++  V RVR AE++L   GK   LTEA AR L KLMAYKDEYEVARL+TD  F
Sbjct: 1007 NAAYAQTYQAFVERVRVAEASL---GK-TTLTEAVARYLFKLMAYKDEYEVARLHTDTGF 1062

Query: 1052 LDKLRNQFEGEPGRDYQLNFWLAPPLMAKRDEKGHLVKRRFGPSTMKLFGVLAKLKGLRG 1111
            L+K+   FEG    D++LN+ LAPPL+A +++KG L K++FGP  +  F +LA+LKGLRG
Sbjct: 1063 LNKVNAMFEG----DFKLNYHLAPPLIASKNDKGELQKQQFGPWMLTGFRLLARLKGLRG 1118

Query: 1112 GVFDVFGKTAERRTERALIGEYRALLEELTRGLSAANHATAITLASLPDDIRGFGHVKDD 1171
              FDVFG++ ERR ERALI EYRA +EE+  GL+   HA A+ +A +P+ I+G+GHVK  
Sbjct: 1119 TPFDVFGRSDERREERALIAEYRASIEEVLTGLTPEKHAAAVEIARIPELIKGYGHVKAR 1178

Query: 1172 NLAKVRTRWTALLEQFRHPETAQR 1195
            +L   R +W AL++ FR P + Q+
Sbjct: 1179 HLVTARPQWAALMQAFRQPVSLQK 1202


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: 3305
Number of extensions: 115
Number of successful extensions: 12
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: 1206
Length adjustment: 47
Effective length of query: 1150
Effective length of database: 1159
Effective search space:  1332850
Effective search space used:  1332850
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 24 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