Alignments for a candidate for ofo in Rhizorhabdus wittichii RW1

GapMind for catabolism of small carbon sources

Alignments for a candidate for ofo in Rhizorhabdus wittichii RW1

Align 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) (characterized)
to candidate WP_041379293.1 SWIT_RS15320 indolepyruvate ferredoxin oxidoreductase family protein

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



>NCBI__GCF_000016765.1:WP_041379293.1
          Length = 1155

 Score = 1031 bits (2665), Expect = 0.0
 Identities = 566/1182 (47%), Positives = 742/1182 (62%), Gaps = 52/1182 (4%)

Query: 20   VSLEDKYTLERGRVYISGTQALVRLPMLQRERDRAAGLNTAGFISGYRGSPLGALDQSLW 79
            VSL+DK+T++RGR+ I+GTQA+ R  + QRE DR  GL+TAGFI+GYRGSPLG +D +LW
Sbjct: 12   VSLDDKWTVDRGRIVINGTQAIARTLLAQRELDRRRGLSTAGFITGYRGSPLGNVDMTLW 71

Query: 80   KAKQHLAAHDIVFQAGLNEDLAATSVWGSQQVNMYPDARFEGVFGMWYGKGPGVDRTSDV 139
                 L+A  IVFQ G+NED+AAT+V GSQQ++  P AR +GVF  WYGKGPGVDR+ D 
Sbjct: 72   SIGDRLSAAGIVFQPGVNEDIAATAVHGSQQIDAVPGARHDGVFAAWYGKGPGVDRSGDA 131

Query: 140  FKHANSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKACGLPVLYPSNVQEYLDYGLH 199
            FKH N AG+   GGVL+  GDDH  KSST+AHQSE    A  +P LYP+NVQE L++GL 
Sbjct: 132  FKHGNYAGAHAKGGVLLFYGDDHGGKSSTVAHQSEQAIAASLIPSLYPANVQEILEFGLL 191

Query: 200  AWAMSRYSGLWVSMKCVTDVVESSASVELDPHRVEIVLPQ-----DFILPPGGLNIRWPD 254
             +AMSRYSG W++MKCV ++ E +A++++D    +  LP      +  +  G  N     
Sbjct: 192  GFAMSRYSGSWIAMKCVNEIAEQTATIDIDLPAFDPALPAMDGVGEVSIGQGVFN----- 246

Query: 255  PPLEQEARLLDYKWYAGLAYVRANKIDRIEIDSPHARFGIMTGGKAYLDTRQALANLGLD 314
             PL  E+ +LD++     A+VR NKIDR    +   R GI+T GK+Y D   ALA LGLD
Sbjct: 247  -PLGDESLVLDHRLPRVHAFVRGNKIDRTVFRAGKPRLGIVTAGKSYGDVCAALALLGLD 305

Query: 315  DETCARIGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKRQIMEYALKEELYNWRDDV 374
            + + +  GI LYKVGC+WPLE  G  AFA+G   ILVVEEK+  +E  + E + N  D  
Sbjct: 306  ETSASEAGISLYKVGCIWPLEPIGLVAFAKGHDAILVVEEKKSFLEQQIAEIIVN--DPQ 363

Query: 375  RPKVYGKFDEKDNAGGEWSIPQSNWLLPAHYELSPAIIARAIATRLDKFELPADVRARIA 434
            RP ++GK DE+  +           L  ++  L PA IAR IA RL +     D     +
Sbjct: 364  RPMLFGKRDEEGRS-----------LFSSNLPLEPAGIARVIAERLGRLGQAIDGAPMPS 412

Query: 435  ARIAVIEAKEKAMAVPRVAAERKPWFCSGCPHNTSTNVPEGSRALAGIGCHYMTVWMDRS 494
               A ++A            +R P+FCSGCPHN ST VPEGS ++ GIGCH M  ++   
Sbjct: 413  TDGAPVDAD---------LPKRSPFFCSGCPHNRSTRVPEGSTSMTGIGCHTMAHFVRPK 463

Query: 495  TSTF-SQMGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSGLLAIRASIAAGVNITYKILY 553
             +   +QMGGEG  W+G APF   KH+F N+GDGTY+HSGLLAIRA++AA VNITYKILY
Sbjct: 464  EALLPTQMGGEGGNWLGLAPFTDTKHIFQNMGDGTYYHSGLLAIRAAVAARVNITYKILY 523

Query: 554  NDAVAMTGGQPIDGKLSVQDVANQVAAEGARKIVVVTDEPEKYSAAIKLPQGVEVHHRDE 613
            NDAVAMTGGQP+DG +SV ++A QV  EG  K+ +++D+P ++    +LP  V + HRDE
Sbjct: 524  NDAVAMTGGQPVDGPISVAEIARQVRDEGVSKVWLLSDDPMRHRGNRELPAEVIIGHRDE 583

Query: 614  LDRIQRELREVPGATILIYDQTCATEKRRRRKRGTYPDPAKRAFINDAVCEGCGDCSVKS 673
            LDR+QR LR++PG T+LIY+QTCA EKRRRRKRGT+PDPAKR FI  +VCEGCGDCSV+S
Sbjct: 584  LDRVQRALRDMPGCTVLIYEQTCAAEKRRRRKRGTFPDPAKRQFIAKSVCEGCGDCSVQS 643

Query: 674  NCLSVEPLETELGTKRQINQSSCNKDFSCVNGFCPSFVTAEGAQVKKPERHGVSMDNLPA 733
             C+S+ P++T  G KR+I+QSSCNKD+SCV GFCPSFVT  GA+ +KPE   +  D    
Sbjct: 644  TCVSLMPVDTAFGRKREIDQSSCNKDYSCVEGFCPSFVTIHGAEPRKPETVALGQDLFAG 703

Query: 734  LPQPA-LPGLEHPYGVLVTGVGGTGVVTIGGLLGMAAHLENKGVTVLDMAGLAQKGGAVL 792
            LP P   P     Y +++ G+GGTGVVT+G LLGMAAH+E   +++ DM GL+QK GAV 
Sbjct: 704  LPDPVPAPIAGASYNLMIAGIGGTGVVTVGALLGMAAHIEGLAMSLFDMTGLSQKNGAVF 763

Query: 793  SHVQIAAHPDQLHATRIAMGEADLVIGCDAIVSAIDDVISKTQVGRTRAIVNTAQTPTAE 852
            SHV+I+  P+ +HA R+  GEADLV+  D + +   +  +   +GRTRAI N A  PT  
Sbjct: 764  SHVRISRRPEDIHAQRLGAGEADLVMAFDLVAALSPEAATTFSIGRTRAIANAAVAPTVA 823

Query: 853  F-IKNPKWQFPGLSAEQDVRNAVGEACDFINASGLAVALIGDAIFTNPLVLGYAWQKGWL 911
            F  +      P L   +  R    +    ++AS LA+A++GD I  N  ++G A Q+G L
Sbjct: 824  FQFQRDFAADPKLLLARLRRGIAQDGLATVDASMLALAILGDTIGANLFLVGMAAQRGLL 883

Query: 912  PLSLDALVRAIELNGTAVEKNKAAFDWGRHMAHDPEHVLSLTGKLRNTAEGAEVVKLPTS 971
            P+ + A+ RAIELNG A+  N  A   GR  A DP+ V +L       AE          
Sbjct: 884  PIPIAAIERAIELNGVAISFNLRALRLGRLFAADPDRVTALVPVPERQAE---------- 933

Query: 972  SGALLEKLIAHRAEHLTAYQDAAYAQTFRDTVSRVRAAESALVGNGKPLPLTEAAARNLS 1031
                L+ LI HR  HLT YQDA  A  +R  V RV   E+ +    +   LT A ARN +
Sbjct: 934  EDMSLDALITHRGAHLTDYQDARLADRYRALVDRVGRREAEVAPASQ--ALTRAVARNHA 991

Query: 1032 KLMAYKDEYEVARLYTDPIFLDKLRNQFEGEPGRDYQLNFWLAPPLMAKRDEKGHLVKRR 1091
            +L+AYKDEYEVARL + P  LD++R  F  + GR   + F LAPPL AK    G   KR 
Sbjct: 992  RLLAYKDEYEVARLLSQPALLDEIRRTF-ADGGR---IAFNLAPPLFAKVGLNGRPGKRE 1047

Query: 1092 FGPSTMKLFGVLAKLKGLRGGVFDVFGKTAERRTERALIGEYRALLEELTRGLSAANHAT 1151
             G   +    +LA+ + +RG  +D FG+TAERR ERALIG+Y AL++ +   L   N   
Sbjct: 1048 LGAWMIPAMRLLARFRAIRGRWYDPFGQTAERRMERALIGDYEALVDRVLDRLHPGNLGE 1107

Query: 1152 AITLASLPDDIRGFGHVKDDNLAKVRTRWTALLEQFRHPETA 1193
            A TL SL D+IRGFG VK   +   R R     EQF     A
Sbjct: 1108 ATTLLSLADEIRGFGPVKAAAVHSYRERLAEAEEQFSRDSRA 1149


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: 3281
Number of extensions: 160
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: 1155
Length adjustment: 47
Effective length of query: 1150
Effective length of database: 1108
Effective search space:  1274200
Effective search space used:  1274200
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 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