Alignments for a candidate for ofo in Azoarcus sp. BH72

GapMind for catabolism of small carbon sources

Alignments for a candidate for ofo in Azoarcus sp. BH72

Align 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) (characterized)
to candidate WP_011767155.1 AZO_RS17245 MFS transporter

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



>NCBI__GCF_000061505.1:WP_011767155.1
          Length = 1198

 Score = 1406 bits (3639), Expect = 0.0
 Identities = 721/1191 (60%), Positives = 880/1191 (73%), Gaps = 41/1191 (3%)

Query: 14   RRALANVSLEDKYTLERGRVYISGTQALVRLPMLQRERDRAAGLNTAGFISGYRGSPLGA 73
            +R L N  L+D+YTL  GRVY+SG QALVRL M+Q ERD AAGL+TAGF+SGYRGSPLG 
Sbjct: 28   QRPLGN--LDDRYTLVSGRVYLSGYQALVRLLMIQSERDAAAGLHTAGFVSGYRGSPLGG 85

Query: 74   LDQSLWKAKQHLAAHDIVFQAGLNEDLAATSVWGSQQVNMYPDARFEGVFGMWYGKGPGV 133
            LDQ+LWKAKQHLAAHDIVFQ G+NEDLAAT+VWGSQQVN+ P AR++GVF MWYGKGPGV
Sbjct: 86   LDQTLWKAKQHLAAHDIVFQPGVNEDLAATAVWGSQQVNLSPQARYDGVFAMWYGKGPGV 145

Query: 134  DRTSDVFKHANSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKACGLPVLYPSNVQEY 193
            DR  DVF+HAN+AGS+R GGVLV+AGDDHAAKSSTL HQ++H FK+  +PVL P+ VQEY
Sbjct: 146  DRCGDVFRHANAAGSARFGGVLVIAGDDHAAKSSTLPHQTDHFFKSMMMPVLAPAGVQEY 205

Query: 194  LDYGLHAWAMSRYSGLWVSMKCVTDVVESSASVELDPHRVEIVLPQDFILPPGGLNIRWP 253
            +D+G+H +A+SRYSG WV+ K + D VE+SASV++DP RV++  P DF LPP GLNIRWP
Sbjct: 206  IDFGVHGYALSRYSGCWVAFKALADTVETSASVDVDPQRVQVATPTDFPLPPDGLNIRWP 265

Query: 254  DPPLEQEARLLDYKWYAGLAYVRANKIDRIEIDSPHARFGIMTGGKAYLDTRQALANLGL 313
            DPPL QE RLL +K YA LAY RAN+++R+ IDSP  R GI+T GK+YLD RQA  +LG+
Sbjct: 266  DPPLVQEKRLLHFKLYAALAYARANRLNRVVIDSPAPRLGIITSGKSYLDVRQAFDDLGI 325

Query: 314  DDETCARIGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKRQIMEYALKEELYNWRDD 373
            DD   A IGIRLYKVG VWPLE+ G R FAEGL EILVVEEKRQ++EY LKEELYNWR+D
Sbjct: 326  DDALAAEIGIRLYKVGMVWPLESDGVRQFAEGLDEILVVEEKRQLLEYQLKEELYNWRED 385

Query: 374  VRPKVYGKFDEKDN----AGGEWSIPQSNWLLPAHYELSPAIIARAIATRLDKFELPADV 429
            VRP+V GKFDEK      A G+ +I   +WLLPA  EL+PA+IAR IA R+++F     V
Sbjct: 386  VRPRVIGKFDEKGEWARIARGDGTIDHGDWLLPAAGELNPALIARVIAGRIERF----FV 441

Query: 430  RARIAARIAVIEAKEKAMAVPRVAAERKPWFCSGCPHNTSTNVPEGSRALAGIGCHYMTV 489
              RI AR+A +EAK+  +A    + +R P FCSGCPHN ST VPEGSRALAGIGCHYM  
Sbjct: 442  SERIRARLAFLEAKDHTLAQRVFSIDRVPTFCSGCPHNISTRVPEGSRALAGIGCHYMVT 501

Query: 490  WM-DRSTSTFSQMGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSGLLAIRASIAAGVNIT 548
            WM DR T TF+QMGGEGV W+GQAPF  ++H+FANLGDGTYFHSGLLAIR ++AAGVNIT
Sbjct: 502  WMPDRRTGTFTQMGGEGVPWVGQAPFTHERHIFANLGDGTYFHSGLLAIRQAVAAGVNIT 561

Query: 549  YKILYNDAVAMTGGQPIDGKLSVQDVANQVAAEGARKIVVVTDEPEKYSAAIKLPQGVEV 608
            YKIL+NDAVAMTGGQP++G L+V  +  Q+ AEG   IVVVTD  E+   A  LP  V +
Sbjct: 562  YKILFNDAVAMTGGQPVEGGLTVPKIVRQLQAEGVHNIVVVTDGTERGYGAADLPH-VPI 620

Query: 609  HHRDELDRIQRELREVPGATILIYDQTCATEKRRRRKRGTYPDPAKRAFINDAVCEGCGD 668
             HRDELD IQRELRE  G T LIYDQTCA EKRRRRKRGT+PDPA+R FIN+AVCEGCGD
Sbjct: 621  RHRDELDAIQRELRESGGVTALIYDQTCAAEKRRRRKRGTFPDPARRVFINEAVCEGCGD 680

Query: 669  CSVKSNCLSVEPLETELGTKRQINQSSCNKDFSCVNGFCPSFVTAEGAQVKKPERHGVSM 728
            C V+SNC+S+ P+ETE G KR I+QSSCNKD+SC+NGFCPSF+T EG + +K +      
Sbjct: 681  CGVQSNCMSILPVETEFGRKRAIDQSSCNKDYSCLNGFCPSFITVEGGRPRKGQALETDE 740

Query: 729  DNLPALPQPALPGLEHPYGVLVTGVGGTGVVTIGGLLGMAAHLENKGVTVLDMAGLAQKG 788
                 LP P LP  E P+G+LVTGVGGTGVVTIG L+GMAAHL+ KGVTVLDM GLAQKG
Sbjct: 741  SRFGELPPPRLPTTETPFGILVTGVGGTGVVTIGALIGMAAHLDGKGVTVLDMTGLAQKG 800

Query: 789  GAVLSHVQIAAHPDQLHATRIAMGEADLVIGCDAIVSAIDDVISKTQVGRTRAIVNTAQT 848
            G+V SH++IA  P+ LHA RIA GEAD VIG D IVSA  + + K    RTRA+VN A+T
Sbjct: 801  GSVFSHIRIAERPEDLHAVRIAAGEADAVIGGDIIVSASVEALGKMSAERTRAVVNLAET 860

Query: 849  PTAEFIKNPKWQFPGLSAEQDVRNAVGEA-----CDFINASGLAVALIGDAIFTNPLVLG 903
            PT++F +NP W+FP       ++ A+GEA      DFI+A  +A  L+GDAI TN  +LG
Sbjct: 861  PTSDFARNPDWRFP----LDQMKTAIGEATRPGGVDFIDAQSIATRLLGDAIATNLFLLG 916

Query: 904  YAWQKGWLPLSLDALVRAIELNGTAVEKNKAAFDWGRHMAHDPEHVLSLTGKLRNTAEGA 963
            YAWQKG +P+ L+AL++AI LNG A+  N+ AF WGR  AHDP  VL+L       A  A
Sbjct: 917  YAWQKGLVPVRLEALMQAITLNGVALALNRKAFLWGRRAAHDPAAVLAL-------AHPA 969

Query: 964  EVVKL--PTSSGALLEKLIAHRAEHLTAYQDAAYAQTFRDTVSRVRAAESALVGNGKPLP 1021
              V+L  PT     L+++++ RA  L+AYQDAAYA  +R  VS+VR  E+  V       
Sbjct: 970  PPVRLHPPT-----LDEVVSIRANFLSAYQDAAYADRYRRLVSQVREQEARAVSPAS-TR 1023

Query: 1022 LTEAAARNLSKLMAYKDEYEVARLYTDPIFLDKLRNQFEGEPGRDYQLNFWLAPPLMAKR 1081
            L EA ARN  KL+AYKDEYEVARLY DP F  ++   FEG    DY++ F LAPP +A+ 
Sbjct: 1024 LAEAVARNYFKLLAYKDEYEVARLYVDPAFWARVDETFEG----DYEVRFHLAPPFLARL 1079

Query: 1082 DEK-GHLVKRRFGPSTMKLFGVLAKLKGLRGGVFDVFGKTAERRTERALIGEYRALLEEL 1140
            D + G + K+ FG + + +F  LA+L+ +RG  +D+FG TAERR ERALI +Y A + EL
Sbjct: 1080 DPRTGRIPKKAFGAAVLHVFRWLARLRRVRGTRWDIFGYTAERRAERALITQYEADVAEL 1139

Query: 1141 TRGLSAANHATAITLASLPDDIRGFGHVKDDNLAKVRTRWTALLEQFRHPE 1191
               LS    A A+ +A +PD IRGFG +K  N+ +   R  ALL  +R  E
Sbjct: 1140 LASLSEPRLALAVDIAGIPDVIRGFGPIKARNMEEAARRRAALLATWRDAE 1190


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: 3488
Number of extensions: 129
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: 1198
Length adjustment: 47
Effective length of query: 1150
Effective length of database: 1151
Effective search space:  1323650
Effective search space used:  1323650
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 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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
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