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 branched-chain ketoacid ferredoxin reductase (EC 1.2.7.7) active on 4-methyl-2-oxopentanoate, (S)-3-methyl-2-oxopentanoate, or 3-methyl-2-oxobutanoate (characterized)
to candidate WP_011766137.1 AZO_RS12140 MFS transporter

Query= reanno::psRCH2:GFF3452
         (1156 letters)



>NCBI__GCF_000061505.1:WP_011766137.1
          Length = 1194

 Score = 1107 bits (2864), Expect = 0.0
 Identities = 589/1154 (51%), Positives = 764/1154 (66%), Gaps = 22/1154 (1%)

Query: 5    EIRLDDKYRLATGHLYLTGTQALTRLPMLQHQRDQARGLNTGGFISGYRGSPLGGLDKSL 64
            + RL D  +  +G ++LTGTQAL RLP++Q   D A G NTGGFISGYRGSPLG  D+ L
Sbjct: 13   DYRLADSLQAMSGQIFLTGTQALVRLPLMQAALDAAAGRNTGGFISGYRGSPLGAYDQQL 72

Query: 65   WEARDYLKQHAIHFQPGVNEELAATAVWGSQQTNLFPGAKYDGVFAMWYGKGPGVDRAGD 124
            W+A+  L  + I F P VNEEL ATAV G+QQ         DGVFA+WYGKGPGVDRAGD
Sbjct: 73   WKAKALLDANRIRFLPAVNEELGATAVLGTQQVEGDAERTVDGVFAIWYGKGPGVDRAGD 132

Query: 125  VFKHANAAGVSPQGGVLLLAGDDHGCKSSTLPHQSEHAFIAASIPVLNPANVQEILDYGI 184
              +H NA G SP GGVL + GDDHGC SS++PHQS+    A  +PVLNPA+V E+L++G+
Sbjct: 133  ALRHGNAYGASPHGGVLAVIGDDHGCVSSSMPHQSDFTLQAWGLPVLNPASVAEMLEFGL 192

Query: 185  IGWELSRYSGCWVALKTIAENVDSSAVVEVDPLRVQTRIPEDFELPEDGVHIRWPD-PPL 243
             GW LSRYSGCWV LK I+E V+S++ V++D +R +     +F  P  G+H RWPD P L
Sbjct: 193  YGWALSRYSGCWVGLKAISETVESASTVDLDAIRTRFDGVPEFTPPATGLHYRWPDLPSL 252

Query: 244  AQEKRLNLYKIYAARAFARANNLNRVMLDSPNPRLGIITTGKSYLDVRQALDDLGLDEAL 303
              E+RL+  K+ AARAFA AN +++ +  +P   +GI++ GK++LD+ +A   LG+  A 
Sbjct: 253  VIEQRLHA-KLDAARAFAAANPIDKTICAAPQADIGIVSCGKAHLDLLEAFRRLGVSLAD 311

Query: 304  CASVGLRVLKVGMSWPLEPVSVHEFAQGLDEILVVEEKRSIIEDQLTGQLYNWPVSKRPR 363
              + G+R  KVG S+PLE   +  FA GL EILVVEEK  +IE Q+    YN   ++RP 
Sbjct: 312  LEAAGIRFYKVGQSFPLETARMRAFATGLKEILVVEEKGPVIERQIKELFYNADPAERPL 371

Query: 364  VVGEFDEQGNSLLPNLSELTPAMIARVIAKRLAPIYTSDSIQARLAFLA---AKEKALAA 420
            V+G+    G  LL  L EL P+ +  VIA  LA        +A +            L+ 
Sbjct: 372  VIGKSGRDGAPLLSALGELRPSRVIPVIAAWLAGHRPEIEQRAHVVEHVTDFTPPPLLSN 431

Query: 421  RSYSTVRTPHYCSGCPHNSSTKVPEGSRASAGIGCHYMVQWM-DRRTETFTQMGGEGVNW 479
             +    R P++CSGCPHN+STKVPEGS A AGIGCH+M  WM DR T    QMGGEGV+W
Sbjct: 432  EADGVRRVPYFCSGCPHNTSTKVPEGSHAQAGIGCHFMASWMPDRETTGLIQMGGEGVDW 491

Query: 480  IGQAPFTDTPHMFQNLGDGTYFHSGSLAVRAAVAAGVNVTYKILYNDAVAMTGGQPIDGE 539
            +  + FT TPH+FQNLGDGTYFHSG LA+R A+AAG NVTYKILYNDAVAMTGGQP+DG 
Sbjct: 492  VAHSAFTRTPHVFQNLGDGTYFHSGFLAIRQAIAAGTNVTYKILYNDAVAMTGGQPVDGT 551

Query: 540  LRVDQLSRQIFHEGVKRIALVSDEPDKYPSRDTFAPI-TSFHHRRELDAVQRELREFKGV 598
            + VD ++RQ+  EG +R+A+VSDEP+KY   +   P  TSFHHR ELDAVQRELRE KGV
Sbjct: 552  VTVDAIARQVEAEGARRVAVVSDEPEKYDGHEGLFPRGTSFHHRAELDAVQRELREVKGV 611

Query: 599  SVIIYDQTCATEKRRRRKRGKMEDPAKRAFINPAVCEGCGDCGEKSNCLAVLPLETELGR 658
            +V+IYDQTCA EKRRRRK+    DPA+R FIN AVCEGCGDCG++SNCL+++P++T  GR
Sbjct: 612  TVLIYDQTCAAEKRRRRKKQAYPDPARRIFINDAVCEGCGDCGKQSNCLSIVPVDTPFGR 671

Query: 659  KREIDQNACNKDFSCVEGFCPSFVTVHGGGLRKPEAVAGGIEAA-------TLPEPQHPT 711
            KR IDQ++CNKD+SCV GFCPSFV+V GG L+KP   A   +AA       TLP P+   
Sbjct: 672  KRAIDQSSCNKDYSCVNGFCPSFVSVLGGSLKKPTGPA--FDAARLDELVGTLPLPKAWC 729

Query: 712  LDRPWNVLIPGVGGSGVTTLGALLGMAAHLEGKGCTVLDQAGLAQKFGPVTTHVRIAAKQ 771
             D P+++L+ GVGG+GV T+GAL+ MAAHLEGK  +VLD  G AQK G V + VR+ A  
Sbjct: 730  WDAPYDLLVTGVGGTGVVTVGALITMAAHLEGKSASVLDFMGFAQKGGQVLSFVRLGADA 789

Query: 772  SDIYAVRIAAGEADLLLGCDLIVAAGDESLTRLNEQISNAVVNSHESATAEFTRNPDAQV 831
            S +  VRI A +AD +L CDL+V A +++L       +  V N HE  TA F ++PDA +
Sbjct: 790  SVLNQVRIDAQQADAILACDLVVGASNDALLTARHGRTRIVANVHEIQTARFVQDPDADL 849

Query: 832  PGAAMRQAISDAVGADKTHFVDATRLATRLLGDSIATNLFLLGFAYQQGLLPISAEAIEK 891
               A+   +  A G D+    DA  L  R LGD++  N+ L+G+A+Q+GL+P+S  A+++
Sbjct: 850  HVDALLAKMRYAAGDDRLDTCDAQALCARFLGDTMGANILLMGYAWQRGLIPVSLAALDR 909

Query: 892  AIELNGVSAKLNLQAFRWGRRAVLEREAVEQLARPVDMVEPICKTLEEIVDWRVDFLTRY 951
            AIELNGV+  +N  AFR GR A    EA+  LA        +  +L  IV      LT Y
Sbjct: 910  AIELNGVAVAMNRSAFRIGRLAAAGAEALAALAAGPLAQPEVADSLGAIVALHAAHLTGY 969

Query: 952  QSAGLARRYRQLVERV----RDADSAD-DLALSKAVARYYFKLLAYKDEYEVARLYSEPE 1006
            Q+A  A RY   +++V    R A  AD  L L+  VAR Y KLLAYKDEYEVARLY++  
Sbjct: 970  QNAAYAARYTAFIDKVAAAERKALGADAPLRLAPVVARTYGKLLAYKDEYEVARLYTDGR 1029

Query: 1007 FRQQLEAQFEGDYKLQFHLAPAWLAKRDPVTGEPRKRELGPWVLNLFGVLAKFRFLRGTP 1066
            FRQ LEAQFEGDY+LQFH+AP  LAK  P  G P+K + GP ++ L  +LA  R LRGT 
Sbjct: 1030 FRQALEAQFEGDYRLQFHMAPPLLAKPGP-NGRPKKMDFGPRLMPLLRLLAAARGLRGTA 1088

Query: 1067 LDPFGYGHDRRVERQLISEYEKTVDELLAQLKPTNYRTAVAIAALPEQIRGYGPVKERSI 1126
             D FG   +RR+ER+L ++Y + +D LL +L       AV  A L E +RG+GPVK  ++
Sbjct: 1089 FDLFGRSEERRMERELAADYARAIDALLPRLAADTVDAAVEFAGLAEGVRGFGPVKLANL 1148

Query: 1127 AKARQQEKLLREQL 1140
               +Q+E++L   L
Sbjct: 1149 RTVKQRERVLLHTL 1162


Lambda     K      H
   0.319    0.136    0.405 

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: 3100
Number of extensions: 110
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: 1156
Length of database: 1194
Length adjustment: 47
Effective length of query: 1109
Effective length of database: 1147
Effective search space:  1272023
Effective search space used:  1272023
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 (21.8 bits)
S2: 58 (26.9 bits)

This GapMind analysis is from Sep 24 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
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