Alignments for a candidate for ofo in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for ofo in Herbaspirillum seropedicae SmR1

Align 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) (characterized)
to candidate HSERO_RS12755 HSERO_RS12755 MFS transporter

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



>FitnessBrowser__HerbieS:HSERO_RS12755
          Length = 1180

 Score = 1322 bits (3422), Expect = 0.0
 Identities = 684/1181 (57%), Positives = 852/1181 (72%), Gaps = 36/1181 (3%)

Query: 17   LANVSLEDKYTLERGRVYISGTQALVRLPMLQRERDRAAGLNTAGFISGYRGSPLGALDQ 76
            LA VSL+DKYT   G +Y+SG QALVRLP+LQ+ RDRAAGLNTAGFISGYRGSPLG LD+
Sbjct: 14   LAPVSLDDKYTATTGAIYLSGIQALVRLPLLQQIRDRAAGLNTAGFISGYRGSPLGGLDE 73

Query: 77   SLWKAKQHLAAHDIVFQAGLNEDLAATSVWGSQQVNMYPDARFEGVFGMWYGKGPGVDRT 136
            +LW A+ HLAAH + FQ G+NED+AAT+VWG+QQV +   + ++GV+ MWYGKGPGVDR 
Sbjct: 74   ALWHAQPHLAAHRVKFQPGVNEDMAATAVWGTQQVKLIGPSDYDGVYAMWYGKGPGVDRC 133

Query: 137  SDVFKHANSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKACGLPVLYPSNVQEYLDY 196
             DV KH N AG+S HGGVL++AGDDH A SSTL HQS+HIF A  +P+LYP NVQEYLD 
Sbjct: 134  GDVLKHMNHAGTSAHGGVLLVAGDDHGAYSSTLPHQSDHIFSASMIPMLYPCNVQEYLDL 193

Query: 197  GLHAWAMSRYSGLWVSMKCVTDVVESSASVELDPHRVEIVLPQDFILPPGGLNIRWPDPP 256
            GLH WAMSRYSG  V  K + D VESSASV+ DP RV+I LP DF++P GGLN R     
Sbjct: 194  GLHGWAMSRYSGCVVGFKALADTVESSASVDADPFRVQIRLPSDFVMPEGGLNARLSTDT 253

Query: 257  L-----EQEARLLDYKWYAGLAYVRANKIDRIEIDSPHARFGIMTGGKAYLDTRQALANL 311
            L     +QEA + DYK YA LAY RAN+++R+ IDSP AR GI+  GK+YLD  +AL+ L
Sbjct: 254  LGVQARKQEALMQDYKIYAALAYARANRLNRVMIDSPKARLGIIASGKSYLDVLEALSEL 313

Query: 312  GLDDETCARIGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKRQIMEYALKEELYNWR 371
            G+D+   A IG+RL+KV   WPLE  G R FA+GL EILVVEEKRQ++EY LKE+LYNWR
Sbjct: 314  GIDEAFAAEIGLRLFKVSMPWPLEPDGVREFAQGLDEILVVEEKRQMVEYQLKEQLYNWR 373

Query: 372  DDVRPKVYGKFDEKDNAGGEWSIPQSNWLLPAHYELSPAIIARAIATRLDKFELPADVRA 431
            DDVRP+V GKFDEK    GEW  P+  WLL +  + S A IAR IA R+ +F   +D+  
Sbjct: 374  DDVRPRVIGKFDEK----GEWVAPRGEWLLTSKADFSVAQIARVIAARIARFH-TSDL-- 426

Query: 432  RIAARIAVIEAKEKAMAVPRVAAERKPWFCSGCPHNTSTNVPEGSRALAGIGCHYM-TVW 490
             I AR+A ++AK+  ++       R  ++CSGCPHN+ST VPEGS ALAGIGCH M T  
Sbjct: 427  -IKARLAFLDAKDAVLSKAVNTPPRPAYYCSGCPHNSSTRVPEGSFALAGIGCHVMATAI 485

Query: 491  MDRSTSTFSQMGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSGLLAIRASIAAGVNITYK 550
                    + MGGEG  WIGQAPF+   HVFANLGDGTYFHSG LAIRA++AA VN+TYK
Sbjct: 486  YPEFNKLTTHMGGEGAPWIGQAPFSKVPHVFANLGDGTYFHSGYLAIRAAVAAKVNMTYK 545

Query: 551  ILYNDAVAMTGGQPIDGKLSVQDVANQVAAEGARKIVVVTDEPEKYSAAIKLPQGVEVHH 610
            ILYNDAVAMTGGQP+DG +SV  +A Q+AAEG ++I +V+++P +Y+    LP  V VH 
Sbjct: 546  ILYNDAVAMTGGQPVDGTVSVPMIAQQMAAEGVQRIALVSEDPGRYADRSSLPAAVTVHD 605

Query: 611  RDELDRIQRELREVPGATILIYDQTCATEKRRRRKRGTYPDPAKRAFINDAVCEGCGDCS 670
            R ++D +QRELRE+PG T++IYDQTCA EKRRRRK+G YPDP +R FIN AVCEGCGDC 
Sbjct: 606  RKDMDAVQRELRELPGVTVIIYDQTCAAEKRRRRKKGDYPDPNQRLFINAAVCEGCGDCG 665

Query: 671  VKSNCLSVEPLETELGTKRQINQSSCNKDFSCVNGFCPSFVTAEGAQVKKPERHGVS--- 727
            V+SNC S+ PLET+LG KR I+QSSCNKD+SCV GFCPSFVT  G +++K  R GVS   
Sbjct: 666  VQSNCTSILPLETDLGRKRVIDQSSCNKDYSCVKGFCPSFVTVTGGKLRK-SRTGVSRQE 724

Query: 728  -MDNLPALPQPALPGLEHPYGVLVTGVGGTGVVTIGGLLGMAAHLENKGVTVLDMAGLAQ 786
              D+   LPQP LP  + P+ +L+ G+GGTGV+TIG L+GMAAHLE KG +VLDM G++Q
Sbjct: 725  ERDDFGLLPQPVLPACDTPFNILINGIGGTGVITIGALMGMAAHLEGKGASVLDMTGMSQ 784

Query: 787  KGGAVLSHVQIAAHPDQLHATRIAMGEADLVIGCDAIVSAIDDVISKTQVGRTRAIVNTA 846
            K G+V SHV+IAA  D + A RIA GEADLV+GCD + +   D ISK + GRTRA+VN  
Sbjct: 785  KNGSVTSHVRIAARRDAIRAQRIATGEADLVLGCDMLTAGAFDAISKMRPGRTRAVVNLH 844

Query: 847  QTPTAEFIKNPKWQFPGLSAEQDVRNAVGEACDFINASGLAVALIGDAIFTNPLVLGYAW 906
            Q P  +F +NP W+FP    +  +  +VG+  DFI+A+ LA AL+GD+I TN  +LGYAW
Sbjct: 845  QQPPGQFARNPDWEFPVEEVKALIVESVGQQADFIDATRLATALMGDSIATNLFMLGYAW 904

Query: 907  QKGWLPLSLDALVRAIELNGTAVEKNKAAFDWGRHMAHDPEHVLSLTGKLRNTAEGAEVV 966
            Q+G LPL+  +L+RAIELNG AV+ NK AF WGR  A D   V  +    +       ++
Sbjct: 905  QRGELPLTEASLLRAIELNGVAVQANKTAFAWGRRAAVDLARVEQIAVPAQPV-----LL 959

Query: 967  KLPTSSGALLEKLIAHRAEHLTAYQDAAYAQTFRDTVSRVRAAESALVGNGKPLPLTEAA 1026
             LP S    L++LI  R   LT YQDAAYA  F + V  VRAAE+AL G+ K   L  A 
Sbjct: 960  HLPQS----LDQLIKRRVSLLTDYQDAAYAAQFLEVVEAVRAAEAAL-GSDK---LATAV 1011

Query: 1027 ARNLSKLMAYKDEYEVARLYTDPIFLDKLRNQFEGEPGRDYQLNFWLAPPLMAKRDEKGH 1086
            ARNLS+LMAYKDEYEVARLYT+  F  +L  QFEG    D+ L+F LAPPL+A++D +GH
Sbjct: 1012 ARNLSRLMAYKDEYEVARLYTNGQFQKELAQQFEG----DFSLSFHLAPPLLARKDGQGH 1067

Query: 1087 LVKRRFGPSTMKLFGVLAKLKGLRGGVFDVFGKTAERRTERALIGEYRALLEELTRGLSA 1146
            L+K R+G   M+ F +LA++KGLRGG+ D+FG T ERR ER LI +YR L+ +L   L+A
Sbjct: 1068 LLKARYGGWVMQAFKLLARMKGLRGGLLDLFGHTEERRMERELIVQYRQLVLDLLPRLTA 1127

Query: 1147 ANHATAITLASLPDDIRGFGHVKDDNLAKVRTRWTALLEQF 1187
            AN ATAI LA LP+ +RG+GHVK   +  +RTR   LL  F
Sbjct: 1128 ANLATAIELAQLPEQVRGYGHVKLKAVHAMRTRQQQLLAVF 1168


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: 3109
Number of extensions: 111
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: 1180
Length adjustment: 47
Effective length of query: 1150
Effective length of database: 1133
Effective search space:  1302950
Effective search space used:  1302950
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 Apr 09 2024. 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 2024 update 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