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 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) (characterized)
to candidate WP_050464564.1 AKL27_RS19660 indolepyruvate ferredoxin oxidoreductase

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



>NCBI__GCF_001189915.1:WP_050464564.1
          Length = 1204

 Score = 1494 bits (3869), Expect = 0.0
 Identities = 760/1211 (62%), Positives = 908/1211 (74%), Gaps = 33/1211 (2%)

Query: 1    MNAPLTPPVSDAIRRALANVSLEDKYTLERGRVYISGTQALVRLPMLQRERDRAAGLNTA 60
            MNAPL    +   R  L ++SL+DKYTLERG V+++G QALVRLPMLQR+ D  AGLNTA
Sbjct: 1    MNAPL----NSGQRLLLDDISLDDKYTLERGHVFMTGIQALVRLPMLQRQADVRAGLNTA 56

Query: 61   GFISGYRGSPLGALDQSLWKAKQHLAAHDIVFQAGLNEDLAATSVWGSQQVNMYPDARFE 120
            GF +GYRGSPLG +D +  KAK++L A+ I F  G+NEDLAATSVWG+QQVN++P A+++
Sbjct: 57   GFFTGYRGSPLGTVDLTAAKAKKYLEANHIKFHPGMNEDLAATSVWGTQQVNLFPGAQYD 116

Query: 121  GVFGMWYGKGPGVDRTSDVFKHANSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKAC 180
            GVFG+WYGKGPGVDR  DVFKHAN AG+SRHGGVLV+AGDDHAAKSST AHQSEHI  AC
Sbjct: 117  GVFGLWYGKGPGVDRCGDVFKHANMAGTSRHGGVLVIAGDDHAAKSSTTAHQSEHILNAC 176

Query: 181  GLPVLYPSNVQEYLDYGLHAWAMSRYSGLWVSMKCVTDVVESSASVELDPHRVEIVLPQD 240
            G+PVLYPS VQEYLDYGLH WAMSRY+GLWVS+KCVTD+VES  SV +DP RV+IVLP+D
Sbjct: 177  GIPVLYPSTVQEYLDYGLHGWAMSRYTGLWVSLKCVTDIVESGMSVNIDPDRVKIVLPED 236

Query: 241  FILPPGGLNIRWPDPPLEQEARLLDYKWYAGLAYVRANKIDRIEIDSPHARFGIMTGGKA 300
            F LPPGGLNIR PD  LEQE R+  YKWYA LAY R N++++I  DSP AR GI+T GK+
Sbjct: 237  FQLPPGGLNIRQPDTVLEQETRMNVYKWYAALAYARVNQLNKIIWDSPRARIGIITAGKS 296

Query: 301  YLDTRQALANLGLDDETCARIGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKRQIME 360
            YLDTRQAL +LG+D+     IGIRLYK+G  WPLEA G R FA+GL+EILVVEEKRQI+E
Sbjct: 297  YLDTRQALEDLGIDENVARDIGIRLYKIGMTWPLEAEGVRNFAQGLEEILVVEEKRQILE 356

Query: 361  YALKEELYNWRDDVRPKVYGKFDEKDNAGGEWS-IPQ---SNWLLPAHYELSPAIIARAI 416
            Y LKEELYNWRDDVRP+V GKFD+     GEWS  PQ    NWLLPA YEL+PA IARAI
Sbjct: 357  YQLKEELYNWRDDVRPRVVGKFDDT----GEWSGSPQQGHGNWLLPATYELNPAQIARAI 412

Query: 417  ATRLDKFELPADVRARIAARIAVIEAKEKAMAVPRVA---AERKPWFCSGCPHNTSTNVP 473
            ATR+ K+     V  R+  RIA +EAKE A+ V   A    +R P FCSGCPHNTST +P
Sbjct: 413  ATRISKYFAGHPVEQRVKVRIAYLEAKEGALNVSTKADPTKDRIPHFCSGCPHNTSTRLP 472

Query: 474  EGSRALAGIGCHYMTVWMDRSTSTFSQMGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSG 533
            EGSR LAGIGCHYM  WMDR +S F+ MGGEGV W+GQAPF  +KHVFANLGDGTYFHSG
Sbjct: 473  EGSRGLAGIGCHYMVTWMDRESSLFTHMGGEGVTWVGQAPFTSEKHVFANLGDGTYFHSG 532

Query: 534  LLAIRASIAAGVNITYKILYNDAVAMTGGQPIDGKLSVQDVANQVAAEGARKIVVVTDEP 593
            LLA+RAS+AA VNITYKILYNDAVAMTGGQ  DG L    ++ Q+AAE    I+VVTDEP
Sbjct: 533  LLAVRASVAASVNITYKILYNDAVAMTGGQEFDGPLDPAMISRQLAAENVTPIIVVTDEP 592

Query: 594  EKYSAAIKLPQGVEVHHRDELDRIQRELREVPGATILIYDQTCATEKRRRRKRGTYPDPA 653
            +KY +     +GV + HR ELD +QRELRE PG + +IYDQTCA+EKRRRRKR  YPDPA
Sbjct: 593  DKYPSGTPWAEGVTIRHRSELDAVQRELREKPGVSAMIYDQTCASEKRRRRKRNEYPDPA 652

Query: 654  KRAFINDAVCEGCGDCSVKSNCLSVEPLETELGTKRQINQSSCNKDFSCVNGFCPSFVTA 713
            KRA IN+AVCEGCGDCSV+SNCLSVEPLETE G KRQINQSSCNKD+SCVNGFCPSFVT 
Sbjct: 653  KRAVINEAVCEGCGDCSVQSNCLSVEPLETEFGRKRQINQSSCNKDYSCVNGFCPSFVTV 712

Query: 714  EGAQVKKPERHGVSMDN------LPALPQPALPGLEHPYGVLVTGVGGTGVVTIGGLLGM 767
            EG Q+KKP+R               ALPQP LP L  PYG++VTG+GGTGV+TIG +L M
Sbjct: 713  EGGQLKKPKRIEAPGSKPGPDAATYALPQPVLPPLTQPYGIIVTGIGGTGVITIGQILAM 772

Query: 768  AAHLENKGVTVLDMAGLAQKGGAVLSHVQIAAHPDQLHATRIAMGEADLVIGCDAIVSAI 827
            AAH+E K  +VLDM+GLAQKGG V+SHV+++ H D +++TR+  G ADLVIGCD IV+A 
Sbjct: 773  AAHVEGKACSVLDMSGLAQKGGPVMSHVRLSDHADDIYSTRVGTGAADLVIGCDVIVTAG 832

Query: 828  DDVISKTQVGRTRAIVNTAQTPTAEFIKNPKWQFPGLSAEQDVRNAVG-EACDFINASGL 886
             D +S+   GRT A VN AQTPTA F++NP WQFP  SA+Q ++ A G +    I+A G+
Sbjct: 833  RDALSRMGEGRTHAAVNAAQTPTAAFVRNPDWQFPAASAQQSIQEACGKDRVAMIDAGGI 892

Query: 887  AVALIGDAIFTNPLVLGYAWQKGWLPLSLDALVRAIELNGTAVEKNKAAFDWGRHMAHDP 946
            A AL+GDAI TN  +LGYAWQ GW+PLS  AL+RAIELN  +V  NK AF WGR  AHD 
Sbjct: 893  AAALLGDAIATNMFMLGYAWQHGWVPLSEAALLRAIELNALSVAFNKQAFGWGRAAAHDA 952

Query: 947  EHVLSLT-GKLRNTAEGAEVV--KLPTSSGALLEKLIAHRAEHLTAYQDAAYAQTFRDTV 1003
            E VL +      +T   A+V+  K P S    LE  I  R E L+AYQDAAY++ ++D V
Sbjct: 953  EAVLQVARSNGMSTQPQAQVIDFKHPPS----LEHQITTRGEFLSAYQDAAYSRHYQDVV 1008

Query: 1004 SRVRAAESALVGNGKPLPLTEAAARNLSKLMAYKDEYEVARLYTDPIFLDKLRNQFEGEP 1063
            +RVR AE+AL   GKPL LT A A+ L KLMAYKDEYEVARL+T   F +K+   FEG  
Sbjct: 1009 ARVRTAETALGDAGKPLRLTHAVAQYLFKLMAYKDEYEVARLHTATAFRNKISAMFEG-- 1066

Query: 1064 GRDYQLNFWLAPPLMAKRDEKGHLVKRRFGPSTMKLFGVLAKLKGLRGGVFDVFGKTAER 1123
              DY+L F LAPPL A+ D KG+L+K+ FG   M+ FGVLAK K LRG  FD FG TAER
Sbjct: 1067 --DYKLKFHLAPPLFARHDAKGYLIKQEFGSWMMQAFGVLAKFKFLRGTAFDPFGHTAER 1124

Query: 1124 RTERALIGEYRALLEELTRGLSAANHATAITLASLPDDIRGFGHVKDDNLAKVRTRWTAL 1183
            + ERALI +Y+  LE L   L+ AN   A+ +AS+P++IRG+GH+K+ +L   +++   L
Sbjct: 1125 KQERALIAQYQRTLEILLARLNEANLTQAVAIASIPEEIRGYGHIKERHLLAAQSKHAEL 1184

Query: 1184 LEQFRHPETAQ 1194
            +  F   ET Q
Sbjct: 1185 MRMFDAGETPQ 1195


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: 3588
Number of extensions: 141
Number of successful extensions: 6
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: 1204
Length adjustment: 47
Effective length of query: 1150
Effective length of database: 1157
Effective search space:  1330550
Effective search space used:  1330550
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.

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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