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_RS21380 HSERO_RS21380 MFS transporter

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



>FitnessBrowser__HerbieS:HSERO_RS21380
          Length = 1199

 Score = 1486 bits (3848), Expect = 0.0
 Identities = 753/1195 (63%), Positives = 898/1195 (75%), Gaps = 26/1195 (2%)

Query: 1    MNAPLTPPVSDAIRRALANVSLEDKYTLERGRVYISGTQALVRLPMLQRERDRAAGLNTA 60
            MNAPL  P     R  L +VSL+DKYTLERGRV+++G QALVRLPMLQR+ D+ AGLNTA
Sbjct: 1    MNAPL--PAGQ--RLLLDDVSLDDKYTLERGRVFMTGIQALVRLPMLQRQYDQRAGLNTA 56

Query: 61   GFISGYRGSPLGALDQSLWKAKQHLAAHDIVFQAGLNEDLAATSVWGSQQVNMYPDARFE 120
            GFI+GYRGSPLGA+DQ+  KA+++L A  I F  G+NEDLAATSVWG+QQVN++  A+++
Sbjct: 57   GFITGYRGSPLGAVDQTAEKARKYLEAKQIKFHPGMNEDLAATSVWGTQQVNLFKGAQYD 116

Query: 121  GVFGMWYGKGPGVDRTSDVFKHANSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKAC 180
            GVF +WYGKGPGVDR  DVFKHAN AG+SRHGGVLV+AGDDHAAKSST AHQSEHI KAC
Sbjct: 117  GVFSLWYGKGPGVDRCGDVFKHANMAGTSRHGGVLVIAGDDHAAKSSTAAHQSEHILKAC 176

Query: 181  GLPVLYPSNVQEYLDYGLHAWAMSRYSGLWVSMKCVTDVVESSASVELDPHRVEIVLPQD 240
            G+PVLYPS+VQEYLDYGLH WAMSRY+GLWV+MKCVTD+VES  SV +DP RV+I LP D
Sbjct: 177  GIPVLYPSSVQEYLDYGLHGWAMSRYTGLWVAMKCVTDLVESGMSVMIDPERVQIQLPAD 236

Query: 241  FILPPGGLNIRWPDPPLEQEARLLDYKWYAGLAYVRANKIDRIEIDSPHARFGIMTGGKA 300
            F LPP GLNIR PD  L QEAR+++YKWYA LAY RANK++RI  DSP AR GI+T GK+
Sbjct: 237  FELPPDGLNIRQPDTVLGQEARMINYKWYAALAYARANKLNRIIWDSPRARIGIITAGKS 296

Query: 301  YLDTRQALANLGLDDETCARIGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKRQIME 360
            YLDTRQAL +LG+D++    IGIRLYKVG  WPLEA G R FA+GL EILVVEEKRQI+E
Sbjct: 297  YLDTRQALEDLGIDEQAARDIGIRLYKVGMTWPLEAEGVREFAQGLDEILVVEEKRQILE 356

Query: 361  YALKEELYNWRDDVRPKVYGKFDEKDNAGGEWSIPQ----SNWLLPAHYELSPAIIARAI 416
            Y LKEELYNWRDDVRP+V GKFD+     GEWS  Q     NWLLPA YEL+PA IARAI
Sbjct: 357  YQLKEELYNWRDDVRPRVVGKFDDT----GEWSGSQREGHGNWLLPATYELNPAQIARAI 412

Query: 417  ATRLDKFELPADVRARIAARIAVIEAKEKAMAV---PRVAAERKPWFCSGCPHNTSTNVP 473
            ATR+ ++     V  ++ AR+A +EAKE  + +   P    +R P FCSGCPHNTST +P
Sbjct: 413  ATRISRYFAGHPVEQQVRARVAYLEAKEATLNISSKPDPDKDRIPHFCSGCPHNTSTKLP 472

Query: 474  EGSRALAGIGCHYMTVWMDRSTSTFSQMGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSG 533
            EGSR LAGIGCHYM  WMDR T  F+ MGGEGV W+GQAPF  +KHVFANLGDGTYFHSG
Sbjct: 473  EGSRGLAGIGCHYMVTWMDRETKLFTHMGGEGVTWVGQAPFTDEKHVFANLGDGTYFHSG 532

Query: 534  LLAIRASIAAGVNITYKILYNDAVAMTGGQPIDGKLSVQDVANQVAAEGARKIVVVTDEP 593
            LLA+RAS+AA VNITYKILYNDAVAMTGGQ  DG L    ++ Q+AAE  R I+VVTDEP
Sbjct: 533  LLAVRASVAAKVNITYKILYNDAVAMTGGQEFDGPLDPAMISRQLAAENVRPIIVVTDEP 592

Query: 594  EKYSAAIKLPQGVEVHHRDELDRIQRELREVPGATILIYDQTCATEKRRRRKRGTYPDPA 653
            +KY    +  +GV + HR ELD +QRELRE PG + +IYDQTCA+EKRRRRKR  YPDPA
Sbjct: 593  DKYPVGTQWAEGVTIRHRSELDAVQRELREQPGVSAMIYDQTCASEKRRRRKRNAYPDPA 652

Query: 654  KRAFINDAVCEGCGDCSVKSNCLSVEPLETELGTKRQINQSSCNKDFSCVNGFCPSFVTA 713
            KRA IN+AVCEGCGDCSV+SNCLSVEPLETE G KRQINQSSCNKD+SCVNGFCPSFVT 
Sbjct: 653  KRAVINEAVCEGCGDCSVQSNCLSVEPLETEFGRKRQINQSSCNKDYSCVNGFCPSFVTV 712

Query: 714  EGAQVKKPERHGVSM-DNLPALPQPALPGLEHPYGVLVTGVGGTGVVTIGGLLGMAAHLE 772
            EG Q+KKP R    +   LP+LP+P LPGL  PYG+LVTGVGGTGV+TIG ++ MAAH+E
Sbjct: 713  EGGQLKKPARAQADVGPALPSLPEPVLPGLAQPYGILVTGVGGTGVITIGQIIAMAAHVE 772

Query: 773  NKGVTVLDMAGLAQKGGAVLSHVQIAAHPDQLHATRIAMGEADLVIGCDAIVSAIDDVIS 832
             +  +VLDM+GLAQKGG V+SHV++A     +H+TR+  G ADLVIGCD IV+A  D +S
Sbjct: 773  GRACSVLDMSGLAQKGGPVMSHVRVAEDAAHIHSTRVGTGMADLVIGCDVIVTASRDALS 832

Query: 833  KTQVGRTRAIVNTAQTPTAEFIKNPKWQFPGLSAEQDVRNAVG-EACDFINASGLAVALI 891
            +   GRT A VN+ Q PTA F++NP WQFP  S+E ++  A G +    ++A  +A AL+
Sbjct: 833  RMGEGRTHAAVNSTQMPTAAFVRNPDWQFPTASSEGEIARACGRDNLSLVDAGRIATALM 892

Query: 892  GDAIFTNPLVLGYAWQKGWLPLSLDALVRAIELNGTAVEKNKAAFDWGRHMAHDPEHVLS 951
            GDAI TN  +LGYAWQKGW+PLS  AL+RAIELN   VE NK AF WGR  AHD   VL+
Sbjct: 893  GDAIATNMFMLGYAWQKGWVPLSEAALLRAIELNALQVEFNKQAFAWGRAAAHDVAFVLA 952

Query: 952  LTGKLRNTAEGAEVVKLPTSSGALLEKLIAHRAEHLTAYQDAAYAQTFRDTVSRVRAAES 1011
              G+   +A+  E  + PT     L++L+  R   LT Y +AAYA+++RD V +VRA ES
Sbjct: 953  AAGRNGMSAQVIEFKRTPT-----LDELVERRVAFLTDYLNAAYARSYRDFVEQVRARES 1007

Query: 1012 ALVGNGKPLPLTEAAARNLSKLMAYKDEYEVARLYTDPIFLDKLRNQFEGEPGRDYQLNF 1071
            AL   G+ L L+ A A  L KLMAYKDEYEVARL+ DP F  K+   FEG    DY+L F
Sbjct: 1008 ALGEAGRGLKLSRAVASYLFKLMAYKDEYEVARLHADPAFRAKIAGMFEG----DYKLRF 1063

Query: 1072 WLAPPLMAKRDEKGHLVKRRFGPSTMKLFGVLAKLKGLRGGVFDVFGKTAERRTERALIG 1131
             LAPPL+AKRD+KGHL K+ FG   M +FGVLA+L+ LRG   D F  T ERR ERALI 
Sbjct: 1064 HLAPPLLAKRDDKGHLRKQAFGSWMMPVFGVLARLRFLRGTALDPFAYTEERRQERALIT 1123

Query: 1132 EYRALLEELTRGLSAANHATAITLASLPDDIRGFGHVKDDNLAKVRTRWTALLEQ 1186
            EYRA L  L   L+  N      +A +P++IRG+GHVK+ +L     +  ALL Q
Sbjct: 1124 EYRATLSRLLDRLTPENLEQITAVARIPEEIRGYGHVKERHLKAAMEKQAALLAQ 1178


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: 3469
Number of extensions: 130
Number of successful extensions: 6
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: 1199
Length adjustment: 47
Effective length of query: 1150
Effective length of database: 1152
Effective search space:  1324800
Effective search space used:  1324800
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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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:

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:

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:

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:

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