Alignments for a candidate for ofo in Methylocapsa aurea KYG T

GapMind for catabolism of small carbon sources

Alignments for a candidate for ofo in Methylocapsa aurea KYG T

Align 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) (characterized)
to candidate WP_036262550.1 DL86_RS13695 indolepyruvate ferredoxin oxidoreductase

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



>NCBI__GCF_000746085.1:WP_036262550.1
          Length = 1167

 Score = 1169 bits (3024), Expect = 0.0
 Identities = 612/1187 (51%), Positives = 794/1187 (66%), Gaps = 34/1187 (2%)

Query: 13   IRRALANVSLEDKYTLERGRVYISGTQALVRLPMLQRERDRAAGLNTAGFISGYRGSPLG 72
            + + L   SL DKY L + R+++SG QA+VRL ++Q+E DR AGL TAGFISGY GSPLG
Sbjct: 11   LHQDLKTTSLTDKYDLTKQRIFVSGPQAVVRLLLMQKELDRRAGLTTAGFISGYPGSPLG 70

Query: 73   ALDQSLWKAKQHLAAHDIVFQAGLNEDLAATSVWGSQQVNMYPDARFEGVFGMWYGKGPG 132
             LD +  +AK+    +DI+FQ GLNEDLAAT++WG+QQ  M  + RFEGVFG+WYGKGPG
Sbjct: 71   GLDHNFIRAKRVFDENDILFQPGLNEDLAATAIWGAQQAEMRGEGRFEGVFGLWYGKGPG 130

Query: 133  VDRTSDVFKHANSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKACGLPVLYPSNVQE 192
            VDR+ DVF+H N AG+S+HGGVL L GDDH A+SST AHQSE  F    +P+L P+ VQE
Sbjct: 131  VDRSGDVFRHVNLAGTSKHGGVLALMGDDHTAESSTTAHQSEFTFVDVMMPILSPAGVQE 190

Query: 193  YLDYGLHAWAMSRYSGLWVSMKCVTDVVESSASVELDPHRVEIVLPQDFILPPGGLNIRW 252
             +DYGL  +AMSR++G WV +KC+ D +ES+ S+++   R+    P DF +P GGLNIR 
Sbjct: 191  IVDYGLLGYAMSRFTGAWVGLKCLKDTIESTGSIDVSLDRITPRAPVDFAMPLGGLNIRA 250

Query: 253  PDPPLEQEARLLDYKWYAGLAYVRANKIDRIEIDS-PHARFGIMTGGKAYLDTRQALANL 311
             D   EQE RL ++K  A LA++RAN+++RI      +A+ G++  GK+YLD RQA+ +L
Sbjct: 251  RDNIHEQERRLQNFKRDAMLAWLRANRLNRIVTSGGANAKIGVIAAGKSYLDVRQAMDDL 310

Query: 312  GLDDETCARIGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKRQIMEYALKEELYNWR 371
            G+D+     +G+RL+K+GC WPLE  G R FA GL+ I+VVEEKR ++E  ++EELY   
Sbjct: 311  GIDEVGANALGLRLFKIGCTWPLEPLGLREFARGLELIIVVEEKRSLIETQVREELYGSP 370

Query: 372  DDVRPKVYGKFDEKDNAGGEWSIPQSNWLLPAHYELSPAIIARAIATRLDKFELPADVRA 431
            +  +P   GK DE              WL P    L    IA AI  RL +F        
Sbjct: 371  N--QPVCIGKKDEN-----------GRWLFPVTGALDANDIAIAIGRRLLRFS----GGE 413

Query: 432  RIAARIAVIEAKEKAMAVPRVAAERKPWFCSGCPHNTSTNVPEGSRALAGIGCHYMTVWM 491
            ++  R+  +E  + ++A       R P+FC+GCPHNTST VPEG RA AGIGCHYM  WM
Sbjct: 414  KLEQRLQRLEQAQASLASSEDLGVRSPYFCAGCPHNTSTKVPEGMRAYAGIGCHYMAQWM 473

Query: 492  DRSTSTFSQMGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSGLLAIRASIAAGVNITYKI 551
            DRST  F+QMGGEG  WIG+APF+  +H+F NLGDGTY HSG+LA+R ++A+GVNITYKI
Sbjct: 474  DRSTEGFTQMGGEGANWIGEAPFSKRQHIFQNLGDGTYCHSGILALRFAVASGVNITYKI 533

Query: 552  LYNDAVAMTGGQPIDGKLSVQDVANQVAAEGARKIVVVTDEPEKYSAAIKLPQGVEVHHR 611
            L+N+ VAMTGGQ ++G L+V  +A QVAAE   +IVVVTDEP KY A+++ P+G+ +  R
Sbjct: 534  LFNEVVAMTGGQRLEGGLTVDMIARQVAAENVARIVVVTDEPNKYPASLQWPKGLTIRPR 593

Query: 612  DELDRIQRELREVPGATILIYDQTCATEKRRRRKRGTYPDPAKRAFINDAVCEGCGDCSV 671
             ELD +QREL  +PG T+LIYDQTCA+EKRRRRKRG   DP KR  IN+ VCEGCGDC V
Sbjct: 594  QELDDVQRELAALPGVTVLIYDQTCASEKRRRRKRGEMADPDKRVIINELVCEGCGDCGV 653

Query: 672  KSNCLSVEPLETELGTKRQINQSSCNKDFSCVNGFCPSFVTAEGAQVKKPERHGVSMDNL 731
            KSNC+SV+PLETE G KR I+QSSCNKDFSC+NGFCP+ VT  GA+ KK    G    + 
Sbjct: 654  KSNCVSVQPLETEFGRKRVIDQSSCNKDFSCLNGFCPALVTVHGARPKKALVKGDC--DF 711

Query: 732  PALPQPALPGL-EHPYGVLVTGVGGTGVVTIGGLLGMAAHLENKGVTVLDMAGLAQKGGA 790
            P  P+PA+  +   PYG+LVTGVGGTGVVTIG +LGMAAHLE KG   +DMAGLAQKGGA
Sbjct: 712  PTPPRPAISAIGARPYGILVTGVGGTGVVTIGAILGMAAHLEGKGCGSIDMAGLAQKGGA 771

Query: 791  VLSHVQIAAHPDQLHATRIAMGEADLVIGCDAIVSAIDDVISKTQVGRTRAIVNTAQTPT 850
            V SHV+IA  P+ +HA R+A GEADLV+GCD +VS    V++  + G T  +VNTA+   
Sbjct: 772  VYSHVKIAERPEDIHAIRVAAGEADLVLGCDLVVSGSKKVLAAMRRGETGVLVNTAEIYP 831

Query: 851  AEFIKNPKWQFPGLSAEQDVRNAVGEACDFINASGLAVALIGDAIFTNPLVLGYAWQKGW 910
             +F     +  P    ++ +R + G+   F++A+G+A AL+G++I  N  +LG+AWQ+G 
Sbjct: 832  GDFTHMADFTLPVAGIKRAIRQSAGDHVSFVDATGVATALLGNSIAANMFMLGHAWQQGL 891

Query: 911  LPLSLDALVRAIELNGTAVEKNKAAFDWGRHMAHDPEHVLSLTGKLRNTAEGAEVVKLPT 970
            +PL   +++RAIELNG AVE NK AF WGR  A D   V ++   LR             
Sbjct: 892  VPLDDASILRAIELNGEAVEMNKQAFLWGRRKAADSAGVEAIAAPLRKPTAAQR------ 945

Query: 971  SSGALLEKLIAHRAEHLTAYQDAAYAQTFRDTVSRVRAAESALVGNGKPLPLTEAAARNL 1030
                 L++LIA R   L AYQD+AYA  +   ++RVR  E A         LTEAAAR L
Sbjct: 946  -QSQSLDELIARRVAFLAAYQDSAYASRYLALINRVREVERAKTPGHD--DLTEAAARYL 1002

Query: 1031 SKLMAYKDEYEVARLYTDPIFLDKLRNQFEGEPGRDYQLNFWLAPPLMAKRDEKGHLVKR 1090
             KLMA KDEYEVARLY D  F  ++   F+GE     +L F LAPP+  +++ KG  VK 
Sbjct: 1003 FKLMAVKDEYEVARLYVDGTFARQVEASFDGE----LKLEFHLAPPIFGRKNAKGEPVKS 1058

Query: 1091 RFGPSTMKLFGVLAKLKGLRGGVFDVFGKTAERRTERALIGEYRALLEELTRGLSAANHA 1150
             FGP  M  F +LA+LK LRG  FD+FG + ERR ER LI +Y  LL E+   LS   HA
Sbjct: 1059 SFGPWIMPAFKLLARLKRLRGTPFDIFGYSTERRIERKLIADYEILLNEILEKLSPDAHA 1118

Query: 1151 TAITLASLPDDIRGFGHVKDDNLAKVRTRWTALLEQFRHPETAQRVA 1197
            TA+ LAS+P+ IRG+GHVK  +L   +     LLEQ R    A ++A
Sbjct: 1119 TAVALASIPEKIRGYGHVKMQHLELAKAEEAVLLEQLRAGAPAVKLA 1165


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: 3129
Number of extensions: 129
Number of successful extensions: 7
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: 1167
Length adjustment: 47
Effective length of query: 1150
Effective length of database: 1120
Effective search space:  1288000
Effective search space used:  1288000
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