Aligments for a candidate for ofo in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Aligments 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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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, or view the source code.

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