Alignments for a candidate for iorAB in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for iorAB in Cupriavidus basilensis 4G11

Align phenylpyruvate ferredoxin oxidoreductase (EC 1.2.7.8) (characterized)
to candidate RR42_RS24125 RR42_RS24125 hypothetical protein

Query= reanno::Marino:GFF880
         (1172 letters)



>FitnessBrowser__Cup4G11:RR42_RS24125
          Length = 1152

 Score =  680 bits (1754), Expect = 0.0
 Identities = 414/1163 (35%), Positives = 620/1163 (53%), Gaps = 58/1163 (4%)

Query: 13   LEDRYLRESGRVFLTGTQALVRIPLMQAALDRKQGLNTAGLVSGYRGSPLGAVDQALWQA 72
            L+ RY  ++   FL G QAL+R+ + Q   D + GL T   V+GY GSPLG++D AL QA
Sbjct: 5    LDARYEADTPLAFLNGNQALIRMIVEQMRSDGETGLRTKAFVTGYPGSPLGSIDIALRQA 64

Query: 73   KDLLDENRIDFVPAINEDLAATILLGTQQVETDEDRQVEGVFGLWYGKGPGVDRAGDALK 132
            K  LD + I    A NE+ A ++L GTQ ++      V+GV G WYGKGPG+DR+GDALK
Sbjct: 65   KRTLDAHGITHRAAQNEEFAVSMLSGTQMLDEHPHPDVDGVVGYWYGKGPGLDRSGDALK 124

Query: 133  HGTTYGSSPHGGVLVVAGDDHGCVSSSMPHQSDVAFMSFFMPTINPANIAEYLEFGLWGY 192
            H    G+S HG V++++G+DH   SS++P+Q + +F    +P + PA++ E+L++GL   
Sbjct: 125  HANFAGTSRHGAVVILSGEDHEAKSSTVPYQQEFSFEHHGIPVLYPASVQEFLDYGLHAA 184

Query: 193  ALSRYSGCWVGFKAISETVESAASVEIPPA------PDF-VTPDDFTAPESGLHYRWPDL 245
            ALSR+SGCWV  K +    +    V++ PA      P+  +    FT      ++R+  +
Sbjct: 185  ALSRFSGCWVALKLVGTLCDGGEVVQLHPAGIRTQIPELQIGGKPFTRM---ANHRFFPV 241

Query: 246  PGPQLETRI-EHKLAAVQAFARANRIDRCLFDNKEARFGIVTTGKGHLDLLEALDLLGID 304
               + E R+ + + AAV A+ARAN ++R +      R GI++ GK   D  +AL+ LG D
Sbjct: 242  TNVETERRLYDERHAAVLAYARANGLNRIVRSAPGDRIGIISAGKSWADTQQALEDLGFD 301

Query: 305  EDKARDMGLDIYKVGMVWPLERRGILDFVHGKEEVLVIEEKRGIIESQIKEYMSEPDRPG 364
                +  G+ + KVG++ P +     +F  G + ++VIEEKR  +E Q+          G
Sbjct: 302  GPALQAQGIRLAKVGLLCPADGAFFREFAEGLQTIVVIEEKRDFLERQV-----AAGAVG 356

Query: 365  EVL--ITGKQDELGRPLIPYVGELSPKLVAGFLAARLGRFFEVD--FSERMAEISAMTTA 420
              +  I GK DE G+ L P  G ++  +VA  LA  L R   +     ER+  +   +  
Sbjct: 357  ATVREILGKHDEHGQRLFPVEGGMTADMVAERLARILARSTPLPERGRERIQYLEGNSVK 416

Query: 421  QDPGGVKRMPYFCSGCPHNTSTKVPEGSKALAGIGCHFMASWMG---RNTESLIQMGGEG 477
            +D     R P +CSGCPHN ST +  G  A    GCH  A+ M    +  E+  Q+GGEG
Sbjct: 417  RDAALPGRAPNYCSGCPHNVSTLLAPGQMAWGAPGCHLFAALMDKPQKRVEATTQLGGEG 476

Query: 478  VNWIGKSRYTGNPHVFQNLGEGTYFHSGSMAIRQAVAAGINITYKILFNDAVAMTGGQPV 537
            + W+G + YT  PH+ QN+G+G  FHS    IR A+  G N+T+K+L N  +A TGGQ  
Sbjct: 477  LPWLGLAPYTSRPHIVQNVGDGALFHSSYQNIRFAITTGANMTFKLLINGVLANTGGQEA 536

Query: 538  DGQITVDRIAQQMAAEGVNRVVVLSDEPEKYDGHHDLFPKDVTFHDRSELDQVQRELRDI 597
             G   +  +A ++  +G +RVV+++ EP++Y       P  +      +L+Q  +EL  I
Sbjct: 537  VGASAIADLAGRLLQDGASRVVLVTKEPDQY--ARVQLPASLVRRSPDQLEQTMKELAAI 594

Query: 598  PGCTVLIYDQTCAAEKRRRRKRKQFPDPAKRAFINHHVCEGCGDCSVQSNCLSVVPRKTE 657
             G T+LIYD  CA E+RRR+KR   P P     +N  VCE CGDC  ++NC+S+    TE
Sbjct: 595  KGVTILIYDGACANERRRRQKRGLLPAPTVFTVVNEEVCENCGDCGAKANCMSLQKVPTE 654

Query: 658  LGRKRKIDQSSCNKDFSCVNGFCPSFVTIEGGQLRKSRGVDTGSVLTRKLADIPAPKLPE 717
             G K +I QS+CN+D +C+ G CPSFVT+E   +   +GV   S+     A IP  +   
Sbjct: 655  FGPKTQIHQSTCNQDQACIQGECPSFVTVE---VESGKGVRKPSLPAIDAASIPEIEPGS 711

Query: 718  MTGSYDLLVGGVGGTGVVTVGQLITMAAHLESRGASVLDFMGFAQKGGTVLSYVRMAPSP 777
            +   Y + + G+GG+GV+T   ++  AA ++       D  G AQK G VLS + +AP+ 
Sbjct: 712  LQAPYHIYIPGLGGSGVLTASAILAQAACMQGLQVKTYDQTGAAQKWGAVLSSLILAPAD 771

Query: 778  DKLHQVRISNGQADAVIACDLVVASSQKALSVLRPNHTRIVANEAELPTADYVLFRDADM 837
               H  ++  G+AD  +A DL+ A     L     NHTR+V N    P  D +      +
Sbjct: 772  RPPHTNKVGIGKADLYLALDLLAAVETNNLKCCDANHTRVVVNAGVFPNGDVIRDSRKTL 831

Query: 838  KADKRLGLLKNAVGEDHFDQLDANGIAEKLMGDTVFSNVMMLGFAWQKGLLPLSEAALMK 897
               +    +  A  ++    LDA  IAE L GD + +N++ +G A+Q G LP+    +  
Sbjct: 832  PTLELCETVAAAGRKESVLTLDARRIAEALFGDFMMTNMVAIGAAYQAGWLPIRAECIEA 891

Query: 898  AIELNGVAIDRNKEAFGWGRLSAVDPSAVTDL-------LDDSNAQVVEVKPE------- 943
            AI LNG  ++ N  AF  GRL    P  V  +       L D   ++  ++ E       
Sbjct: 892  AIGLNGAQVEANTMAFRAGRLWVHAPERVEVMGSLKLHPLADRTERLRALRSEGKLKALA 951

Query: 944  ----------PTLDELINTRHKHLVNYQNQRWADQYRDAVAGVRKAEESL-GETN-LLLT 991
                      P L E +  R   L++YQN  +A +Y   V    +AE +  GE +   +T
Sbjct: 952  RFESHLAKLSPQLRERVQLRFADLIDYQNTAYAARYLGRVTASLQAEAAARGEGHGYEVT 1011

Query: 992  RAVAQQLYRFMAYKDEYEVARLFAETDFMKEVNETFEGDFKVHFHLAPPLLSGETDAQGR 1051
             A+A+ L++ MAYKDEYEVARL   + F K V + F G  ++ ++L PPL        G 
Sbjct: 1012 AAIAESLHKLMAYKDEYEVARLLTLSGFEKRVADMFSGSVRLKYNLQPPL----ARTLGL 1067

Query: 1052 PKKRRFGPWMFRAFRLLAKLRGLRGTAIDPFRYSADRKLDRAMLKDYQSLVDRIGRELNA 1111
              K R G W+  A + LA L+ LRGTA+DPF   A RK +RA+L  Y+ ++    + L+A
Sbjct: 1068 KGKLRVGGWIRPALKTLAALKFLRGTALDPFYALASRKEERALLAWYEGVLGEGLKLLDA 1127

Query: 1112 SNYETFLQLAELPADVRGYGPVR 1134
             N    ++L  LP  +RGY  V+
Sbjct: 1128 HNSAQVVELLRLPTTIRGYETVK 1150


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: 2762
Number of extensions: 110
Number of successful extensions: 11
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: 1172
Length of database: 1152
Length adjustment: 47
Effective length of query: 1125
Effective length of database: 1105
Effective search space:  1243125
Effective search space used:  1243125
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: 58 (26.9 bits)

This GapMind analysis is from Sep 17 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