Alignments for a candidate for ofo in Herbaspirillum autotrophicum IAM 14942

GapMind for catabolism of small carbon sources

Alignments for a candidate for ofo in Herbaspirillum autotrophicum IAM 14942

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_050462465.1 AKL27_RS08740 pyruvate ferredoxin oxidoreductase

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



>NCBI__GCF_001189915.1:WP_050462465.1
          Length = 1168

 Score = 1140 bits (2950), Expect = 0.0
 Identities = 586/1153 (50%), Positives = 782/1153 (67%), Gaps = 24/1153 (2%)

Query: 4    AEIRLDDKYRLATGHLYLTGTQALTRLPMLQHQRDQARGLNTGGFISGYRGSPLGGLDKS 63
            AE +L D  R  +G ++LTGTQAL RL + Q QRD   GLNT GFISGYRGSPLG +D+ 
Sbjct: 6    AEYQLQDNLRQKSGRVFLTGTQALVRLLVTQKQRDADAGLNTAGFISGYRGSPLGAVDQE 65

Query: 64   LWEARDYLKQHAIHFQPGVNEELAATAVWGSQQTNLFPGAKYDGVFAMWYGKGPGVDRAG 123
            +W A   L+ H + F P +NE+L ATAV G+QQ    P    DGVFAMWYGKGPGVDR+G
Sbjct: 66   VWRANALLQAHNVEFLPAINEDLGATAVLGTQQVETNPARTVDGVFAMWYGKGPGVDRSG 125

Query: 124  DVFKHANAAGVSPQGGVLLLAGDDHGCKSSTLPHQSEHAFIAASIPVLNPANVQEILDYG 183
            D  KH NA G SP GGVL++ GDDHGC SS+LPHQSE A +A S+PVLNPAN++E L++G
Sbjct: 126  DAIKHGNAYGSSPHGGVLVVLGDDHGCVSSSLPHQSEQALMAWSMPVLNPANIEEYLEFG 185

Query: 184  IIGWELSRYSGCWVALKTIAENVDSSAVVEVDPLRVQTRIPEDFELPEDGVHIRWPDPPL 243
              GW LSR+SG WV  K I+E V+  AVVE+ P       P+D+  PE G+H RWPD P 
Sbjct: 186  PYGWALSRFSGNWVGFKAISETVEGGAVVEI-PAAASFVTPDDYVYPEQGLHYRWPDLPS 244

Query: 244  AQEKRLNLYKIYAARAFARANNLNRVMLDSPNPRLGIITTGKSYLDVRQALDDLGLDEAL 303
               ++    K+ A +AFAR+N+++R+++ +P+ + GII+ GK+YLD+ +AL  +GLD+A 
Sbjct: 245  LDIEQRVAAKLQAVQAFARSNSIDRLIVAAPHGKFGIISAGKAYLDLLEALQRMGLDQAA 304

Query: 304  CASVGLRVLKVGMSWPLEPVSVHEFAQGLDEILVVEEKRSIIEDQLTGQLYNWPVSKRPR 363
                G+R+ K G+++PLE   +  F +GLDE++VVEEK ++IEDQL   LYN+    RPR
Sbjct: 305  LERHGIRLYKPGLTYPLEQTRLLSFVRGLDEVVVVEEKGAVIEDQLKSLLYNFATDCRPR 364

Query: 364  VVGEFDEQGNSLLPNLSELTPAMIARVIAKRLAPIYTSDSIQARLAFLAAKEKALAARSY 423
            ++G+ D     LL  L EL P+ IA  + + LAP   +  + A L    A +  L+  + 
Sbjct: 365  ILGKTDLNQQPLLSALGELRPSRIAPALIRWLAPKLPALDLAAHLPKFCAAD-LLSNGAD 423

Query: 424  STVRTPHYCSGCPHNSSTKVPEGSRASAGIGCHYMVQWMDRRTETFTQMGGEGVNWIGQA 483
            +  RTP++CSGCPHN+ST+VP GSRA AGIGCH+M  WM R TE  TQMGGEGV W+  +
Sbjct: 424  AVKRTPYFCSGCPHNTSTRVPAGSRALAGIGCHFMATWMQRDTEHLTQMGGEGVTWVAAS 483

Query: 484  PFTDTPHMFQNLGDGTYFHSGSLAVRAAVAAGVNVTYKILYNDAVAMTGGQPIDGELRVD 543
             F    H+FQNLGDGTY+HSG LA+R A+AA  N+TYKILYNDAVAMTGGQP+DG+  V 
Sbjct: 484  RFVSEKHVFQNLGDGTYYHSGYLAIRQAIAARTNITYKILYNDAVAMTGGQPVDGKTSVP 543

Query: 544  QLSRQIFHEGVKRIALVSDEPDKYPSRDTFAPITSFHHRRELDAVQRELREFKGVSVIIY 603
            Q+ +Q+  EG  ++ +V+DEP+KY S      + S HHR ELD  QR+LR+  GV+V++Y
Sbjct: 544  QIVQQVVSEGAVKVIVVTDEPEKYASVKLVDGV-SVHHRSELDYWQRQLRDISGVTVLVY 602

Query: 604  DQTCATEKRRRRKRGKME-----DPAKRAFINPAVCEGCGDCGEKSNCLAVLPLETELGR 658
            DQTCA EKRRRRK+ K +     DP +R  INPAVCEGCGDCG +SNCL++LPLET LGR
Sbjct: 603  DQTCAAEKRRRRKKNKPDQTVFPDPPRRMLINPAVCEGCGDCGVQSNCLSILPLETALGR 662

Query: 659  KREIDQNACNKDFSCVEGFCPSFVTVHGGGLRKPEAVAGGIEAATLPEPQHP-----TLD 713
            KR+I+Q++CNKD+SC+EGFCPSFV+V GG L+KP A +   E       Q+P     + D
Sbjct: 663  KRQIEQSSCNKDYSCIEGFCPSFVSVVGGTLKKPAAASISQEDLERRLQQYPLPAVCSFD 722

Query: 714  RPWNVLIPGVGGSGVTTLGALLGMAAHLEGKGCTVLDQAGLAQKFGPVTTHVRIAAKQSD 773
            +P+ +L+ GVGG+G+ T+GAL+ MAAHLEGKG + LD  G AQK G V +HVR+AA    
Sbjct: 723  KPFEILVAGVGGTGIVTVGALITMAAHLEGKGASTLDFMGFAQKGGAVMSHVRVAASPLA 782

Query: 774  IYAVRIAAGEADLLLGCDLIVAAGDESLTRLNEQISNAVVNSHESATAEFTRNPDAQVPG 833
            +  VRI   +AD +  CDL+VAA  ++L  +    +  V N +E  TAEFT NPDA +  
Sbjct: 783  LNQVRIDLQQADAVFACDLVVAAMPDALAVMRRDHTQVVANENEIPTAEFTHNPDADLRQ 842

Query: 834  AAMRQAISDAVGADKTHFVDATRLATRLLGDSIATNLFLLGFAYQQGLLPISAEAIEKAI 893
             A+ + I  A G   TH ++A   A ++LGD I+ N+ LLG+A+Q+GL+P+   A+ +AI
Sbjct: 843  PALLEKIRTASGDSSTHLLNAQATAAQVLGDPISANILLLGYAWQKGLVPVGLTAMLRAI 902

Query: 894  ELNGVSAKLNLQAFRWGRRAVLEREAVEQLARPVDMVEPI----CKTLEEIVDWRVDFLT 949
            ELN V+  +N +AF  GR    +  AV QL  P+   +PI     ++LE ++D+R ++L 
Sbjct: 903  ELNQVAIAMNKKAFLLGRLLAADANAVRQLTEPLQ--QPIQFALPQSLESMIDFRRNWLH 960

Query: 950  RYQSAGLARRYRQLVERVR----DADSADD-LALSKAVARYYFKLLAYKDEYEVARLYSE 1004
            +YQ+   A RY Q V  V     + D +D    L+KAVARY FKL+AYKDEYEVARL+++
Sbjct: 961  KYQNQAYAERYLQAVRLVEQKEMEVDGSDSKKPLTKAVARYLFKLMAYKDEYEVARLHAD 1020

Query: 1005 PEFRQQLEAQFEGDYKLQFHLAPAWLAKRDPVTGEPRKRELGPWVLNLFGVLAKFRFLRG 1064
            P+F+QQ+ AQFEGDY+LQFHLAP  L KR   +  P KR  G W+L  FGVLA+FRFLR 
Sbjct: 1021 PQFKQQIAAQFEGDYRLQFHLAPPILPKRRKGSDLPAKRTFGSWMLPAFGVLARFRFLRE 1080

Query: 1065 TPLDPFGYGHDRRVERQLISEYEKTVDELLAQLKPTNYRTAVAIAALPEQIRGYGPVKER 1124
            TPLD FGY  +RR ER+L  +Y   VDE++A L   N    + +A LPEQIRGYG VK  
Sbjct: 1081 TPLDIFGYTEERRRERRLRDDYLALVDEIVADLSRENKTMLLKLAQLPEQIRGYGHVKLA 1140

Query: 1125 SIAKARQQEKLLR 1137
            ++ +A +  + LR
Sbjct: 1141 AMDQAERSARELR 1153


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: 2931
Number of extensions: 119
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: 1168
Length adjustment: 47
Effective length of query: 1109
Effective length of database: 1121
Effective search space:  1243189
Effective search space used:  1243189
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