Alignments for a candidate for ofo in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for ofo in Stenotrophomonas chelatiphaga DSM 21508

Align 3-methyl-2-oxobutanoate:ferredoxin oxidoreductase (EC 1.2.7.7) (characterized)
to candidate WP_057508963.1 ABB28_RS12705 indolepyruvate ferredoxin oxidoreductase

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



>NCBI__GCF_001431535.1:WP_057508963.1
          Length = 1229

 Score = 1259 bits (3257), Expect = 0.0
 Identities = 673/1241 (54%), Positives = 818/1241 (65%), Gaps = 78/1241 (6%)

Query: 3    APLTPPVSDAIRRALANVSLEDKYTLERGRVYISGTQALVRLPMLQRERDRAAGLNTAGF 62
            A LT P  D+  +   + +L+ KY  E GR+Y+SG QALVRLP++QR RD AAG+++AGF
Sbjct: 5    AQLTSP--DSADQLDRDYTLDHKYARETGRIYLSGVQALVRLPLMQRLRDAAAGIDSAGF 62

Query: 63   ISGYRGSPLGALDQSLWKAKQHLAAHDIVFQAGLNEDLAATSVWGSQQVNMYPDARFEGV 122
            ISGYRGSPLG  D  LW+A+QHL A  + F  GLNEDL AT VWG+QQ N++P A  +GV
Sbjct: 63   ISGYRGSPLGGFDLELWRARQHLEAARVKFTPGLNEDLGATMVWGTQQTNLFPGANVQGV 122

Query: 123  FGMWYGKGPGVDRTSDVFKHANSAGSSRHGGVLVLAGDDHAAKSSTLAHQSEHIFKACGL 182
            FGMWYGKGPGVDR  DVFKHAN+AG+SR GGVL LA DDHA +SSTL H SE  F +  +
Sbjct: 123  FGMWYGKGPGVDRCGDVFKHANAAGTSRLGGVLALAADDHACRSSTLPHGSEDEFVSAMM 182

Query: 183  PVLYPSNVQEYLDYGLHAWAMSRYSGLWVSMKCVTDVVESSASVELDPHRVEIVLPQDFI 242
            PVL P+ VQ+ LD G+  WAMSRY+G W+  K + + VESSASV++DP    IVLP DF 
Sbjct: 183  PVLNPAGVQDILDMGVLGWAMSRYTGRWIGFKTIAETVESSASVDVDPLARRIVLPDDFE 242

Query: 243  LPPGGLNIRWPDPPLEQEARLLDYKWYAGLAYVRANKIDRIEIDSPHARFGIMTGGKAYL 302
            +P GGLNIRWPDPPL+QE RL  Y   A  A+ RAN IDR  +DSP AR GI+T GK+YL
Sbjct: 243  MPAGGLNIRWPDPPLDQEMRLHRYAVTAAQAFARANGIDRTVLDSPRARLGIVTTGKSYL 302

Query: 303  DTRQALANLGLDDETCARIGIRLYKVGCVWPLEAHGARAFAEGLQEILVVEEKRQIMEYA 362
            D  QAL  LGLD+  CA IGIR+YKVG  WPLE  G   FA+GL++I+VVEEKR  +E  
Sbjct: 303  DVLQALEYLGLDETACADIGIRVYKVGMTWPLEPQGIARFAQGLEDIIVVEEKRAFIERQ 362

Query: 363  LKEELYNWRDD--VRPKVYGKFDEKDNAGGEWSIPQSNWLLPAHYELSPAIIARAIATRL 420
            +KE+ +NW      RP + GK+DE           +  W+LP+  EL+PA IA  I  R+
Sbjct: 363  MKEQFFNWPASWGPRPSIVGKYDE-----------EGEWILPSTGELTPATIAGVIGRRI 411

Query: 421  DKFELPADVRARIAARIAVIEAKEKAMAVPRVAAERKPWFCSGCPHNTSTNVPEGSRALA 480
             KF         I  R+  ++ KE  +A+PR    R P +CSGCPHNTST VPEGSRAL 
Sbjct: 412  QKF----FNNESIEQRLQWMQEKEAELALPRANFPRVPHYCSGCPHNTSTTVPEGSRALG 467

Query: 481  GIGCHYMTVWMDRSTSTFSQMGGEGVAWIGQAPFAGDKHVFANLGDGTYFHSGLLAIRAS 540
            GIGCHYM  WMDRST TF+ MGGEGV W GQA F    HVF NLGDGTYFHSG LAIR S
Sbjct: 468  GIGCHYMVTWMDRSTDTFTHMGGEGVTWAGQAAFTDTPHVFQNLGDGTYFHSGSLAIRQS 527

Query: 541  IAAGVNITYKILYNDAVAMTGGQPIDGKLSVQDVANQVAAEGARKIVVVTDEPEKYS-AA 599
            +AAGVNITYKILYNDAVAMTGGQP+DG LSV D+A Q+ AEG + IVV++D  EK++   
Sbjct: 528  VAAGVNITYKILYNDAVAMTGGQPVDGPLSVPDIARQMRAEGIQTIVVLSDNIEKWTRQR 587

Query: 600  IKLPQGVEVHHRDELDRIQRELREVPGATILIYDQTCATEKRRRRKRGTYPDPAKRAFIN 659
             + P GV  H R  LD +Q+ LREV G +ILIY+QTCATEKRRRRKRG   DPAKR  IN
Sbjct: 588  DQFPDGVAFHDRSALDAVQKRLREVKGVSILIYEQTCATEKRRRRKRGKLEDPAKRVVIN 647

Query: 660  DAVCEGCGDCSVKSNCLSVEPLETELGTKRQINQSSCNKDFSCVNGFCPSFVTAEGAQVK 719
              VCEGCGDC  KS C+SV P ETE G KR I+QS+CNKD+SC  GFCPSFVT  G + +
Sbjct: 648  SLVCEGCGDCGKKSFCVSVLPKETEFGRKRDIDQSNCNKDYSCTTGFCPSFVTVHGGKPR 707

Query: 720  KPERHGVS--MDNLPALPQPALPGLEHPYGVLVTGVGGTGVVTIGGLLGMAAHLENKGVT 777
            K  +   S  +DNLPA   P    LE P+ +L+TGVGGTGVVTIG LLGMA HLE KG +
Sbjct: 708  KGSKRDASTLLDNLPA--PPVRTALEQPWNILITGVGGTGVVTIGALLGMAGHLEGKGSS 765

Query: 778  VLDMAGLAQKGGAVLSHVQIAAHPDQLHATRIAMGEADLVIGCDAIVSAIDDVISKTQVG 837
            VLD  GLAQKGGAV +H++IA  P  +HA RIA GEADLV+GCD +V      +SK + G
Sbjct: 766  VLDQTGLAQKGGAVTTHIRIARTPADIHAVRIAAGEADLVLGCDMVVVNDYWALSKVRAG 825

Query: 838  RTRAIVNTAQTPTAEFIKNPKWQFPGLSAEQDVRNAV-GEACDFINASGLAVALIGDAIF 896
            RT+ ++NT +     F   P  QFP       +R A+ GE+   ++A+ LA AL+GDAI 
Sbjct: 826  RTQVVLNTYEAMPGSFTTRPDMQFPAADIVAGIRVALGGESPLLLDATQLATALLGDAIA 885

Query: 897  TNPLVLGYAWQKGWLPLSLDALVRAIELNGTAVEKNKAAFDWGRHMAHDPEHVLSLTGKL 956
            +N  +LGYAWQ+G +PLS DAL+RAIELNG AV  N+ AF WGR  A DP+ V    G +
Sbjct: 886  SNLFILGYAWQQGLVPLSFDALMRAIELNGAAVAMNQQAFAWGRLAAVDPQAVQQAAGLV 945

Query: 957  RN---TAE-----------------------------------------GAEVVKLPTSS 972
            RN   +AE                                         G +V  LP   
Sbjct: 946  RNGHTSAETTPGPLHALPPGEWESTEWGATAAPRNSSDERELRGLPGNAGDDVAFLPLDD 1005

Query: 973  GAL---LEKLIAHRAEHLTAYQDAAYAQTFRDTVSRVRAAESALVGNGKPLPLTEAAARN 1029
              L   L+++I  RA  L  YQD AYA  +R  V RVR  E   +G      LTE  AR 
Sbjct: 1006 ARLSRSLDEMITRRAAFLVDYQDQAYADRYRSLVDRVRRGEQDTLGGS--TALTETVARY 1063

Query: 1030 LSKLMAYKDEYEVARLYTDPIFLDKLRNQFEGEPGRDYQLNFWLAPPLMAKRDEKGHLVK 1089
            L KLMAYKDEYEVARLYT   F  +L+ QFEGE    YQL F LAPPL AK+D +G L+K
Sbjct: 1064 LFKLMAYKDEYEVARLYTSGDFQRRLQQQFEGE----YQLRFHLAPPLFAKKDAQGRLIK 1119

Query: 1090 RRFGPSTMKLFGVLAKLKGLRGGVFDVFGKTAERRTERALIGEYRALLEELTRGLSAANH 1149
            + +GP  +K FGVLAKLK LRGG  D FG+TAER  ER LI +Y A ++ L  GL     
Sbjct: 1120 KEYGPWMLKAFGVLAKLKFLRGGRLDPFGRTAERVGERQLITDYEATVQLLLDGLDDHRL 1179

Query: 1150 ATAITLASLPDDIRGFGHVKDDNLAKVRTRWTALLEQFRHP 1190
            A A+ +AS+P+ IRG+GHVK+ +L K + R   LL Q+R+P
Sbjct: 1180 ALAVEIASIPEHIRGYGHVKEAHLEKAKAREATLLAQWRNP 1220


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: 3411
Number of extensions: 147
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 1197
Length of database: 1229
Length adjustment: 47
Effective length of query: 1150
Effective length of database: 1182
Effective search space:  1359300
Effective search space used:  1359300
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