GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sibC in Rhodanobacter denitrificans 2APBS1

Align Kynurenine 3-monooxygenase; PfKMO; Kynurenine 3-hydroxylase; EC 1.14.13.9 (characterized)
to candidate WP_007508973.1 R2APBS1_RS11660 FAD-dependent monooxygenase

Query= SwissProt::Q84HF5
         (461 letters)



>NCBI__GCF_000230695.2:WP_007508973.1
          Length = 467

 Score =  442 bits (1138), Expect = e-129
 Identities = 242/464 (52%), Positives = 298/464 (64%), Gaps = 18/464 (3%)

Query: 10  VTIIGAGLAGTLVARLLARNGWQVNLFERRPDPRIETGARGRSINLALAERGAHALRLAG 69
           +T+IG GL G L+A+ LA  G+ V+++E+RPDPR+     GRSINLALAERG  ALR AG
Sbjct: 6   ITLIGGGLVGALLAQQLAGRGFTVDVYEKRPDPRLAGFIGGRSINLALAERGLQALRTAG 65

Query: 70  LEREVLAEAVMMRGRMVHVPGTPPNLQPYGRDDSEVIWSINRDRLNRILLDGAEAAGASI 129
           L  +VL  AVMMRGRMVH       LQ YG DDSEVIWS++R  LN +LLD AEAAGA  
Sbjct: 66  LAEDVLQRAVMMRGRMVHDRDGHSGLQRYGVDDSEVIWSVSRGALNMLLLDAAEAAGARF 125

Query: 130 HFNLGLDSVDFARQRLTLSNVSGERLEKRFHLLIGADGCNSAVRQAMASVVDLGEHLETQ 189
           HF   L   DF RQR+ L++ +G + E+   LLIGADG  S VR AM +   LGE +E+ 
Sbjct: 126 HFGQSLVGADFGRQRIRLADEAGVQHERDAGLLIGADGAGSTVRAAMNAHAPLGERIESL 185

Query: 190 PHGYKELQITPEASA------------QFNLEPNALHIWPHGDYMCIALPNLDRSFTVTL 237
            HGYKEL+I P                QF LEP+ALHIWP G YMCIALPN + SFTVTL
Sbjct: 186 GHGYKELEIPPAGELPAAVLSHSGGRDQFALEPHALHIWPRGGYMCIALPNTEGSFTVTL 245

Query: 238 FLHHQSPAAQPASPCFAQLVDGHAARRFFQRQFPDLSPMLDSLEQDFEHHPTGKLATLRL 297
           FL      AQ A+P FA L D  AA  FF+ QFP L P++    +DF+ HP G L+TL L
Sbjct: 246 FL-----PAQSAAPSFASLPDAAAAAAFFREQFPGLLPLIPRFNEDFDSHPVGTLSTLYL 300

Query: 298 TTWHVGGQAVLLGDAAHPMVPFHGQGMNCALEDAVALAEHLQSA-ADNASALAAFTAQRQ 356
             WH+ G+A+LLGDAAH +VPFHGQGMNC  ED V LA  L  A  D+A   A F   RQ
Sbjct: 301 ERWHLDGRALLLGDAAHAIVPFHGQGMNCGFEDTVVLANLLAEAPGDSADVFAEFQRVRQ 360

Query: 357 PDALAIQAMALENYVEMSSKVASPTYLLERELGQIMAQRQPTRFIPRYSMVTFSRLPYAQ 416
           P+A AI AMALENYVEM   VA P YL +RELG  +A+R P  ++ RY MVTF+ +PYA 
Sbjct: 361 PNADAIAAMALENYVEMRDSVADPHYLAKRELGTKLAERIPGHYMARYRMVTFTHVPYAY 420

Query: 417 AMARGQIQEQLLKFAVANHSDLTSINLDAVEHEVTRCLPPLSHL 460
           A+ RG+ Q+ LL+  + +   +  I+++A        L PL  L
Sbjct: 421 ALERGRAQDHLLEQLLRDTPRVADIDIEAAARLFQSTLEPLPRL 464


Lambda     K      H
   0.321    0.134    0.399 

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: 637
Number of extensions: 21
Number of successful extensions: 4
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: 461
Length of database: 467
Length adjustment: 33
Effective length of query: 428
Effective length of database: 434
Effective search space:   185752
Effective search space used:   185752
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 (21.9 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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:

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:

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:

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:

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