GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ofo in Cupriavidus basilensis 4G11

Align 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) (characterized)
to candidate RR42_RS24125 RR42_RS24125 hypothetical protein

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



>FitnessBrowser__Cup4G11:RR42_RS24125
          Length = 1152

 Score =  741 bits (1912), Expect = 0.0
 Identities = 457/1183 (38%), Positives = 647/1183 (54%), Gaps = 70/1183 (5%)

Query: 21   SLEDKYTLERGRVYISGTQALVRLPMLQRERDRAAGLNTAGFISGYRGSPLGALDQSLWK 80
            SL+ +Y  +    +++G QAL+R+ + Q   D   GL T  F++GY GSPLG++D +L +
Sbjct: 4    SLDARYEADTPLAFLNGNQALIRMIVEQMRSDGETGLRTKAFVTGYPGSPLGSIDIALRQ 63

Query: 81   AKQHLAAHDIVFQAGLNEDLAATSVWGSQQVNMYPDARFEGVFGMWYGKGPGVDRTSDVF 140
            AK+ L AH I  +A  NE+ A + + G+Q ++ +P    +GV G WYGKGPG+DR+ D  
Sbjct: 64   AKRTLDAHGITHRAAQNEEFAVSMLSGTQMLDEHPHPDVDGVVGYWYGKGPGLDRSGDAL 123

Query: 141  KHANSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKACGLPVLYPSNVQEYLDYGLHA 200
            KHAN AG+SRHG V++L+G+DH AKSST+ +Q E  F+  G+PVLYP++VQE+LDYGLHA
Sbjct: 124  KHANFAGTSRHGAVVILSGEDHEAKSSTVPYQQEFSFEHHGIPVLYPASVQEFLDYGLHA 183

Query: 201  WAMSRYSGLWVSMKCVTDVVESSASVELDPHRVEIVLPQDFILPPGG------LNIR-WP 253
             A+SR+SG WV++K V  + +    V+L P  +   +P+   L  GG       N R +P
Sbjct: 184  AALSRFSGCWVALKLVGTLCDGGEVVQLHPAGIRTQIPE---LQIGGKPFTRMANHRFFP 240

Query: 254  DPPLEQEARLLDYKWYAGLAYVRANKIDRIEIDSPHARFGIMTGGKAYLDTRQALANLGL 313
               +E E RL D +  A LAY RAN ++RI   +P  R GI++ GK++ DT+QAL +LG 
Sbjct: 241  VTNVETERRLYDERHAAVLAYARANGLNRIVRSAPGDRIGIISAGKSWADTQQALEDLGF 300

Query: 314  DDETCARIGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKRQIMEYALKEELYNWRDD 373
            D       GIRL KVG + P +    R FAEGLQ I+V+EEKR  +E  +          
Sbjct: 301  DGPALQAQGIRLAKVGLLCPADGAFFREFAEGLQTIVVIEEKRDFLERQVAAGAVG--AT 358

Query: 374  VRPKVYGKFDEKDNAGGEWSIPQSNWLLPAHYELSPAIIARAIATRLDKFELPADVRARI 433
            VR ++ GK DE               L P    ++  ++A  +A  L +   P   R R 
Sbjct: 359  VR-EILGKHDE-----------HGQRLFPVEGGMTADMVAERLARILAR-STPLPERGR- 404

Query: 434  AARIAVIEAKEKAMAVPRVAA--ERKPWFCSGCPHNTSTNVPEGSRALAGIGCHYMTVWM 491
              RI  +E      +V R AA   R P +CSGCPHN ST +  G  A    GCH     M
Sbjct: 405  -ERIQYLEGN----SVKRDAALPGRAPNYCSGCPHNVSTLLAPGQMAWGAPGCHLFAALM 459

Query: 492  D---RSTSTFSQMGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSGLLAIRASIAAGVNIT 548
            D   +     +Q+GGEG+ W+G AP+    H+  N+GDG  FHS    IR +I  G N+T
Sbjct: 460  DKPQKRVEATTQLGGEGLPWLGLAPYTSRPHIVQNVGDGALFHSSYQNIRFAITTGANMT 519

Query: 549  YKILYNDAVAMTGGQPIDGKLSVQDVANQVAAEGARKIVVVTDEPEKYSAAIKLPQGVEV 608
            +K+L N  +A TGGQ   G  ++ D+A ++  +GA ++V+VT EP++Y A ++LP  +  
Sbjct: 520  FKLLINGVLANTGGQEAVGASAIADLAGRLLQDGASRVVLVTKEPDQY-ARVQLPASLVR 578

Query: 609  HHRDELDRIQRELREVPGATILIYDQTCATEKRRRRKRGTYPDPAKRAFINDAVCEGCGD 668
               D+L++  +EL  + G TILIYD  CA E+RRR+KRG  P P     +N+ VCE CGD
Sbjct: 579  RSPDQLEQTMKELAAIKGVTILIYDGACANERRRRQKRGLLPAPTVFTVVNEEVCENCGD 638

Query: 669  CSVKSNCLSVEPLETELGTKRQINQSSCNKDFSCVNGFCPSFVTAE---GAQVKKPERHG 725
            C  K+NC+S++ + TE G K QI+QS+CN+D +C+ G CPSFVT E   G  V+KP    
Sbjct: 639  CGAKANCMSLQKVPTEFGPKTQIHQSTCNQDQACIQGECPSFVTVEVESGKGVRKPSLPA 698

Query: 726  VSMDNLPALPQPALPG-LEHPYGVLVTGVGGTGVVTIGGLLGMAAHLENKGVTVLDMAGL 784
            +   ++P +     PG L+ PY + + G+GG+GV+T   +L  AA ++   V   D  G 
Sbjct: 699  IDAASIPEIE----PGSLQAPYHIYIPGLGGSGVLTASAILAQAACMQGLQVKTYDQTGA 754

Query: 785  AQKGGAVLSHVQIAAHPDQLHATRIAMGEADLVIGCDAIVSAIDDVISKTQVGRTRAIVN 844
            AQK GAVLS + +A      H  ++ +G+ADL +  D + +   + +       TR +VN
Sbjct: 755  AQKWGAVLSSLILAPADRPPHTNKVGIGKADLYLALDLLAAVETNNLKCCDANHTRVVVN 814

Query: 845  TAQTPTAEFIKNPKWQFPGLSAEQDVRNA-VGEACDFINASGLAVALIGDAIFTNPLVLG 903
                P  + I++ +   P L   + V  A   E+   ++A  +A AL GD + TN + +G
Sbjct: 815  AGVFPNGDVIRDSRKTLPTLELCETVAAAGRKESVLTLDARRIAEALFGDFMMTNMVAIG 874

Query: 904  YAWQKGWLPLSLDALVRAIELNGTAVEKNKAAFDWGRHMAHDPEHVLSLTG-KLRNTAEG 962
             A+Q GWLP+  + +  AI LNG  VE N  AF  GR   H PE V  +   KL   A+ 
Sbjct: 875  AAYQAGWLPIRAECIEAAIGLNGAQVEANTMAFRAGRLWVHAPERVEVMGSLKLHPLADR 934

Query: 963  AEVVKLPTSSGAL----------------LEKLIAHRAEHLTAYQDAAYAQTFRDTVSRV 1006
             E ++   S G L                L + +  R   L  YQ+ AYA  +   V+  
Sbjct: 935  TERLRALRSEGKLKALARFESHLAKLSPQLRERVQLRFADLIDYQNTAYAARYLGRVTAS 994

Query: 1007 RAAESALVGNGKPLPLTEAAARNLSKLMAYKDEYEVARLYTDPIFLDKLRNQFEGEPGRD 1066
              AE+A  G G    +T A A +L KLMAYKDEYEVARL T   F  ++ + F G     
Sbjct: 995  LQAEAAARGEGHGYEVTAAIAESLHKLMAYKDEYEVARLLTLSGFEKRVADMFSG----S 1050

Query: 1067 YQLNFWLAPPLMAKRDEKGHLVKRRFGPSTMKLFGVLAKLKGLRGGVFDVFGKTAERRTE 1126
             +L + L PPL      KG   K R G         LA LK LRG   D F   A R+ E
Sbjct: 1051 VRLKYNLQPPLARTLGLKG---KLRVGGWIRPALKTLAALKFLRGTALDPFYALASRKEE 1107

Query: 1127 RALIGEYRALLEELTRGLSAANHATAITLASLPDDIRGFGHVK 1169
            RAL+  Y  +L E  + L A N A  + L  LP  IRG+  VK
Sbjct: 1108 RALLAWYEGVLGEGLKLLDAHNSAQVVELLRLPTTIRGYETVK 1150


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: 2868
Number of extensions: 123
Number of successful extensions: 8
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: 1152
Length adjustment: 47
Effective length of query: 1150
Effective length of database: 1105
Effective search space:  1270750
Effective search space used:  1270750
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 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