GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ofo in Paraburkholderia bryophila 376MFSha3.1

Align 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) (characterized)
to candidate H281DRAFT_01671 H281DRAFT_01671 indolepyruvate ferredoxin oxidoreductase

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



>FitnessBrowser__Burk376:H281DRAFT_01671
          Length = 1184

 Score = 1151 bits (2977), Expect = 0.0
 Identities = 609/1193 (51%), Positives = 791/1193 (66%), Gaps = 30/1193 (2%)

Query: 8    PVSDAIRRALANVSLEDKYTLERGRVYISGTQALVRLPMLQRERDRAAGLNTAGFISGYR 67
            PV +      + VSL+DKY  ERG  Y+SG+ AL+R+ + QR RD  AGLNTAGF+SGYR
Sbjct: 4    PVIEVETAPTSEVSLDDKYRKERGYAYMSGSHALIRVMINQRIRDNDAGLNTAGFVSGYR 63

Query: 68   GSPLGALDQSLWKAKQHLAAHDIVFQAGLNEDLAATSVWGSQQVNMYP-DARFEGVFGMW 126
            GSPL   D +LW A+  L  H I F   +NEDLAAT+VWG+QQ+ ++P ++  EGVF MW
Sbjct: 64   GSPLAGFDTALWSAEAVLKQHQIKFLPAINEDLAATAVWGTQQLALFPQESTVEGVFSMW 123

Query: 127  YGKGPGVDRTSDVFKHANSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKACGLPVLY 186
            YGKGPGVDR+ D  KH N AG+S  GGVLV A DDH AKSST  HQSE    A  +PVLY
Sbjct: 124  YGKGPGVDRSGDALKHGNGAGTSALGGVLVAAADDHTAKSSTFGHQSEQALIAAFIPVLY 183

Query: 187  PSNVQEYLDYGLHAWAMSRYSGLWVSMKCVTDVVESSASVELDPHRVEIVLPQDFILPPG 246
            P++VQ+YLD+G+   AM RYSGLW+ +KCV+DV+E+SA  ++DPHR++I LP        
Sbjct: 184  PASVQDYLDFGVLGIAMGRYSGLWIGLKCVSDVIETSAVADVDPHRIDIRLPDKEFAADD 243

Query: 247  GLNIRWPDPPLEQEARLLDYKWYAGLAYVRANKIDRIEIDSPHARFGIMTGGKAYLDTRQ 306
             L+IR PD   EQE R++  +  A LA+ RAN+++ I I  P ++ GIM  GKAY D  +
Sbjct: 244  DLHIRSPDVWAEQEPRIVRKRLPAALAFCRANRLNSIRIKGPKSKLGIMCAGKAYNDVME 303

Query: 307  ALANLGLDDETCARIGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKRQIMEYALKEE 366
            AL  LGL D+   + G+ + K+G VWPL+    R FA GL E+LVVEEKR I+E  +K+E
Sbjct: 304  ALRLLGLSDDDIEKNGLAVLKIGMVWPLDPTILRDFAAGLDELLVVEEKRPIIEQQIKDE 363

Query: 367  LYNWRDDVRPKVYGKFDEKDNAGGEWSIPQSNWLLPAHYELSPAIIARAIATRLDKFELP 426
            LY+   +  P V          GGEW+      LL + YEL+P  +A AI  RL      
Sbjct: 364  LYSDALNGLPLVRVSGKGSGAIGGEWNRSGEACLLRSDYELTPVEVAGAIVARLRAQAGW 423

Query: 427  ADVRAR-IAARIAVIEAKEKAMAVPRVAAERKPWFCSGCPHNTSTNVPEGSRALAGIGCH 485
             + R R I AR+A +EA  +  AV    A RKP+FCSGCPHNTST VPEGSRA AGIGCH
Sbjct: 424  TETRKREIEARLAALEAVGRVQAV--AGAIRKPFFCSGCPHNTSTRVPEGSRATAGIGCH 481

Query: 486  YMTVWMDRSTSTFSQMGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSGLLAIRASIAAGV 545
            YM   MDR T +++ MGGEGV W+ QA F+  KH+FAN+GDGTYFHSG LAIR ++AA V
Sbjct: 482  YMASSMDRRTESYTHMGGEGVPWVAQAQFSTRKHIFANIGDGTYFHSGSLAIRQAVAARV 541

Query: 546  NITYKILYNDAVAMTGGQPIDGKLSVQDVANQVAAEGARKIVVVTDEPEKYS-AAIKLPQ 604
            ++T+KILYNDA AMTGGQP+DG+L+V  +  QVAAEG R+I VV+D+ E+Y  +      
Sbjct: 542  SMTFKILYNDAAAMTGGQPVDGELTVDGITRQVAAEGVRRIAVVSDDIEQYRISGTTFAA 601

Query: 605  GVEVHHRDELDRIQRELREVPGATILIYDQTCATEKRRRRKRGTYPDPAKRAFINDAVCE 664
            G  VH R ELD +QR LR+  G ++L+YDQTCA+EKRRRRK+GTYPDPAKR  IN  VCE
Sbjct: 602  GTTVHDRSELDAVQRNLRDYEGVSVLVYDQTCASEKRRRRKKGTYPDPAKRVAINSEVCE 661

Query: 665  GCGDCSVKSNCLSVEPLETELGTKRQINQSSCNKDFSCVNGFCPSFVTAEGAQV------ 718
            GCGDCSV+SNCLSVEPL+T LG KRQINQSSCNKDFSCV GFCPSFV+ EG ++      
Sbjct: 662  GCGDCSVQSNCLSVEPLDTPLGRKRQINQSSCNKDFSCVQGFCPSFVSVEGGKLRSSQTK 721

Query: 719  KKPERHGVSMDNLPALPQPALPGLEHPYGVLVTGVGGTGVVTIGGLLGMAAHLENKGVTV 778
            K PE     M + P LP PA P +     +L+ GVGGTGVVTIG LLGMAAHLE +G TV
Sbjct: 722  KSPE---AMMADWPELPYPASPAMTDTVDILINGVGGTGVVTIGNLLGMAAHLEGRGCTV 778

Query: 779  LDMAGLAQKGGAVLSHVQIAAHPDQLHATRIAMGEADLVIGCDAIVSAIDDVISKTQVGR 838
            LDMAGLAQKGGAV SHV++A+  ++++A+RI  G AD++IGCD +V+A  D +S+ + G+
Sbjct: 779  LDMAGLAQKGGAVWSHVRLASKRERMYASRIPSGSADVIIGCDLVVTAAPDTLSRIRKGK 838

Query: 839  TRAIVNTAQTPTAEFIKNPKWQFPGLSAEQDVRNAVG-EACDFINASGLAVALIGDAIFT 897
            TR ++N   +PT+ F+ N  WQ P    +  V +  G +  D+++A  +A   +GD +F+
Sbjct: 839  TRVVINGQTSPTSAFVANRDWQLPEAELKSHVESVCGDDFVDWVDAQEIARRHLGDTVFS 898

Query: 898  NPLVLGYAWQKGWLPLSLDALVRAIELNGTAVEKNKAAFDWGRHMAHDPEHVLSLTGKLR 957
            N ++LG+ WQ+G +PL+ +++ RAIELNG AV+KNK AF  GR +A +P        +  
Sbjct: 899  NAIMLGFVWQQGLIPLARESIERAIELNGQAVKKNKLAFQIGRWLAVNP-------ARFA 951

Query: 958  NTAEGAEVVKLPTSSGALLEKLIAHRAEHLTAYQDAAYAQTFRDTVSRVRAAESALVGNG 1017
               E   V+        +L++LI  R   L AYQ   YA+ +   VS + A   +   +G
Sbjct: 952  AGEEVESVIVWRQKKKVVLDELIQSRVSLLAAYQSERYAREYETFVSEITAQVGS---HG 1008

Query: 1018 KPLPLTEAAARNLSKLMAYKDEYEVARLYTDPIFLDKLRNQFEGEPGRDYQLNFWLAPPL 1077
            K      A A  L KLMAYKDEYEVARLY+ P F   L NQFEG    D+++ ++LAPP+
Sbjct: 1009 KREAFILAVAEGLYKLMAYKDEYEVARLYSLPGFKKSLENQFEG----DFKIRYYLAPPM 1064

Query: 1078 MAKRDEKGHLVKRRFGPSTMKLFGVLAKLKGLRGGVFDVFGKTAERRTERALIGEYRALL 1137
            +++++EKG L+K+ FGP    +F +LA+LK LRG  FD FG TAERR ERALI EYR  +
Sbjct: 1065 LSRKNEKGELIKKEFGPWLGHVFPLLARLKILRGTPFDPFGHTAERRRERALIREYRLWI 1124

Query: 1138 EELTRGLSAANHATAITLASLPDDIRGFGHVKDDNLAKVRTRWTALLEQFRHP 1190
                  L A      I LA LPD IRG+GHVK+  + +V  +   LL     P
Sbjct: 1125 RTALTHL-ADKPDVCIELAKLPDSIRGYGHVKERAIDEVMAKRDTLLAALSAP 1176


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: 3254
Number of extensions: 138
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: 1184
Length adjustment: 47
Effective length of query: 1150
Effective length of database: 1137
Effective search space:  1307550
Effective search space used:  1307550
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