Alignments for a candidate for ofo in Methylobacterium nodulans ORS 2060

GapMind for catabolism of small carbon sources

Alignments for a candidate for ofo in Methylobacterium nodulans ORS 2060

Align 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) (characterized)
to candidate WP_015927043.1 MNOD_RS01415 MFS transporter

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



>NCBI__GCF_000022085.1:WP_015927043.1
          Length = 1161

 Score = 1216 bits (3145), Expect = 0.0
 Identities = 640/1182 (54%), Positives = 813/1182 (68%), Gaps = 43/1182 (3%)

Query: 16   ALANVSLEDKYTLERGRVYISGTQALVRLPMLQRERDRAAGLNTAGFISGYRGSPLGALD 75
            +L  VSLEDKY L R +V+I+GTQA++R+ ++Q+ RDRAAGLNTAGF+SGYRGSP+  LD
Sbjct: 9    SLRPVSLEDKYDLSREQVFITGTQAVIRMLLMQQARDRAAGLNTAGFVSGYRGSPIAGLD 68

Query: 76   QSLWKAKQHLAAHDIVFQAGLNEDLAATSVWGSQQVNMYPDARFEGVFGMWYGKGPGVDR 135
             +L+KA++ L A +IVFQ GLNE+LAAT++WG+QQ  +  + R++GVFG+WYGKGPGVDR
Sbjct: 69   LNLYKARKVLEAANIVFQPGLNEELAATAIWGAQQAEIRGEGRYDGVFGLWYGKGPGVDR 128

Query: 136  TSDVFKHANSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKACGLPVLYPSNVQEYLD 195
              DVF+HAN+AGSSR+GGVL L GDDH A+SSTLAHQSE  F    +P+L P+ VQE LD
Sbjct: 129  AGDVFRHANTAGSSRYGGVLALMGDDHTAESSTLAHQSEFHFVDVMMPILNPAGVQEILD 188

Query: 196  YGLHAWAMSRYSGLWVSMKCVTDVVESSASVELDPHRVEIVLPQDFILPPGGLNIRWPDP 255
            YGL+ +AMSRY G WV+ KCV D +ES+ASV+    RV IV P DF +PPGGLNIR PD 
Sbjct: 189  YGLYGYAMSRYCGTWVAFKCVKDNIESTASVDARLDRVRIVQPDDFAMPPGGLNIRTPDV 248

Query: 256  PLEQEARLLDYKWYAGLAYVRANKIDRIEIDSPHA-RFGIMTGGKAYLDTRQALANLGLD 314
             LEQEARL DYK  A +A+VRAN ++RI +      + G++T GK+YLD RQAL +LGLD
Sbjct: 249  ILEQEARLQDYKRDAMMAFVRANNLNRIILSGGRQPKIGVITVGKSYLDVRQALDDLGLD 308

Query: 315  DETCARIGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKRQIMEYALKEELYNWRDDV 374
            +     +G+RLYKV C WPL      AFAEGL  I+VVEEKR ++E  ++EELY   +  
Sbjct: 309  EVKANDMGLRLYKVACPWPLSQRELLAFAEGLDLIMVVEEKRSLIEVQVREELYGTAN-- 366

Query: 375  RPKVYGKFDEKDNAGGEWSIPQSNWLLPAHYELSPAIIARAIATRLDKFELPADVRARIA 434
            +P   GK DE              WL P    L P  IA A+  RL ++    D    +A
Sbjct: 367  QPICVGKRDEA-----------GRWLFPVKGALDPNDIAVALGERLLRYHRNDD----LA 411

Query: 435  ARIAVIEAKEKAMAVPRVAAERKPWFCSGCPHNTSTNVPEGSRALAGIGCHYMTVWMDRS 494
             R+A +   ++ +A     A R P FC+GCPHN+ST +PEG+RA AGIGCHYM  WM+R 
Sbjct: 412  GRVAALRQAQEILAATTDIAVRTPHFCAGCPHNSSTRIPEGARAYAGIGCHYMAQWMERG 471

Query: 495  TSTFSQMGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSGLLAIRASIAAGVNITYKILYN 554
            T   +QMGGEG  WIG+APF+   HVF NLGDGTY HSG LA+R ++  G  ITYKIL+N
Sbjct: 472  TDGCTQMGGEGANWIGEAPFSKRTHVFQNLGDGTYNHSGSLALRWAVDTGTTITYKILFN 531

Query: 555  DAVAMTGGQPIDGKLSVQDVANQVAAEGARKIVVVTDEPEKYSAAIKLPQGVEVHHRDEL 614
            DAVAMTGGQP +G L+V  +A QV AEG  +I +VTDEP KY + ++ P+G+ +HHRD+L
Sbjct: 532  DAVAMTGGQPHEGGLTVDRIAQQVRAEGVERIALVTDEPHKYPSGMRWPEGLTIHHRDDL 591

Query: 615  DRIQRELREVPGATILIYDQTCATEKRRRRKRGTYPDPAKRAFINDAVCEGCGDCSVKSN 674
            D +QR+L  VPG ++LIYDQTCA EKRRRRKRG +PDP KR  IND VCEGCGDCSV+SN
Sbjct: 592  DTVQRDLATVPGVSVLIYDQTCAAEKRRRRKRGRFPDPDKRVIINDLVCEGCGDCSVQSN 651

Query: 675  CLSVEPLETELGTKRQINQSSCNKDFSCVNGFCPSFVTAEGAQVKKPERHG-VSMDNLP- 732
            C++V+PLETE G KR+I+QSSCNKDFSC+NGFCPSFVT  G    KP  H  V +   P 
Sbjct: 652  CVAVQPLETEFGRKRRIDQSSCNKDFSCLNGFCPSFVTVHGG---KPRTHPLVPLPGTPD 708

Query: 733  -ALPQPALPGLEHPYGVLVTGVGGTGVVTIGGLLGMAAHLENKGVTVLDMAGLAQKGGAV 791
              LP+P LP +E  Y ++VTGVGGTGVVT+G +LGMAAHLE KG+ ++DMAGLAQKGGAV
Sbjct: 709  EGLPEPVLPPIEGTYNIIVTGVGGTGVVTVGAILGMAAHLEGKGLGMIDMAGLAQKGGAV 768

Query: 792  LSHVQIAAHPDQLHATRIAMGEADLVIGCDAIVSAIDDVISKTQVGRTRAIVNTAQTPTA 851
             SHV++A   D +HA R+  G ADL++GCD +V+    V++  + GRT  +VNTA+    
Sbjct: 769  FSHVRLAQAQDDIHAIRVTAGAADLILGCDLVVTGTRKVLAAVRPGRTHVVVNTAEIMPG 828

Query: 852  EFIKNPKWQFPGLSAEQDVRNAVGEA-CDFINASGLAVALIGDAIFTNPLVLGYAWQKGW 910
            +F + P +  P    ++ +R   G A  D  +A+GLAVA +G+AI  N  +LGYAWQ+G 
Sbjct: 829  DFTRRPDFSLPVERIKRVIREKAGPAHADLTDATGLAVAALGNAIAANMFMLGYAWQRGR 888

Query: 911  LPLSLDALVRAIELNGTAVEKNKAAFDWGRHMAHDPEHVLSLTGKLRNTAEGAEVVKLPT 970
            +PLS  A+++AIELN  AV  N AAF WGR  A  PE +            GA      +
Sbjct: 889  VPLSRAAILKAIELNREAVPMNLAAFAWGRRAAAAPETL------------GALKAATAS 936

Query: 971  SSGALLEKLIAHRAEHLTAYQDAAYAQTFRDTVSRVRAAESALVGNGKPLPLTEAAARNL 1030
               A L+ LIA R   LT YQDAAYAQ +   V+ VR  E+A+   G   PLTEA AR+L
Sbjct: 937  DLSADLDTLIARRVAFLTDYQDAAYAQRYARIVASVREREAAVHPGGS--PLTEAVARSL 994

Query: 1031 SKLMAYKDEYEVARLYTDPIFLDKLRNQFEGEPGRDYQLNFWLAPPLMAKRDEK-GHLVK 1089
             KLMAYKDEYEVARLYTD  F  ++RN FEGE G  Y+  F LAPPL+A+ D + G   K
Sbjct: 995  FKLMAYKDEYEVARLYTDGHFEAQIRNTFEGE-GLRYE--FHLAPPLLARTDPRTGRPRK 1051

Query: 1090 RRFGPSTMKLFGVLAKLKGLRGGVFDVFGKTAERRTERALIGEYRALLEELTRGLSAANH 1149
              FGP  +++F +LA++K LRG   D FG T ERR ER LIGE+  L+ E+ R L+ ANH
Sbjct: 1052 MSFGPWVLRVFRMLARMKRLRGTALDPFGYTQERREERRLIGEFETLVAEILRDLTPANH 1111

Query: 1150 ATAITLASLPDDIRGFGHVKDDNLAKVRTRWTALLEQFRHPE 1191
            A A+ LA+LP  IRGFG VK  +LA  +     LL +FR PE
Sbjct: 1112 AVAVGLANLPLTIRGFGPVKAKSLAAAKQEEAVLLTRFRAPE 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: 3222
Number of extensions: 130
Number of successful extensions: 10
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 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