GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuB in Pseudomonas stutzeri RCH2

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate GFF4012 Psest_4085 Biotin carboxylase

Query= reanno::Smeli:SM_b21124
         (662 letters)



>FitnessBrowser__psRCH2:GFF4012
          Length = 471

 Score =  411 bits (1056), Expect = e-119
 Identities = 228/476 (47%), Positives = 291/476 (61%), Gaps = 10/476 (2%)

Query: 1   MFSKLLIANRGEIACRIIRTARRLGIRTVAVYSDADGDALHVALADEAIRIGGAPAAESY 60
           M  KLLIANRGEIA RI+R    +G+R+VAV+S+AD  ALHV  ADEA  IG  P A  Y
Sbjct: 1   MIKKLLIANRGEIAVRIVRACAEMGVRSVAVFSEADRHALHVKRADEAHFIGEDPLA-GY 59

Query: 61  LASAPIVQAARSVGAQAIHPGYGFLSENADFAEAVAEAGMIFVGPPPAAIRAMGLKDAAK 120
           L    +V  A   G  A+HPGYGFLSENA+ A+  AE G+ FVGP    IR MG K  A+
Sbjct: 60  LNPRKLVNLAVETGCDALHPGYGFLSENAELADICAERGIKFVGPSAEVIRRMGDKTEAR 119

Query: 121 ALMERSGVPVVPGYHGEEQDASFLADRAREIGYPVLIKARAGGGGKGMRRVERQEDFGPA 180
             M ++GVPV PG  G  +D +     A  IGYPV++KA +GGGG+G+RR   Q +   A
Sbjct: 120 RSMIKAGVPVTPGTEGNVRDLAEALREAERIGYPVMLKATSGGGGRGIRRCNSQAELESA 179

Query: 181 LEAARREAESAFGDGSVLLERYLTKPRHIEMQVFGDRHGNIVHLFERDCSLQRRHQKVIE 240
                 EA  AFG   V LE+ + +P+HIE Q+  D  GN VHLFERDCS+QRR+QK+IE
Sbjct: 180 YPRVISEATKAFGSAEVFLEKCIVEPKHIEAQILADSFGNTVHLFERDCSIQRRNQKLIE 239

Query: 241 EAPAPGMTAEVRRAMGDAAVRAAQAIGYVGAGTVEFIADVTNGLWPDHFYFMEMNTRLQV 300
            AP+P +T E R  +GD AVRAA+A+GY  AGTVEF+      L     YFMEMNTR+QV
Sbjct: 240 IAPSPQLTPEQRAYIGDLAVRAAKAVGYENAGTVEFL------LADGEVYFMEMNTRVQV 293

Query: 301 EHPVTEAITGIDLVEWQLRVASGEPLPKKQADISMNGWAFEARLYAEDPARGFLPATGRL 360
           EH +TE ITGID+V  Q+R+ASG+PL  KQ DI   G++ + R+ AEDP   FLP  G++
Sbjct: 294 EHTITEEITGIDIVREQIRIASGQPLSVKQEDIQHRGFSLQFRINAEDPRNNFLPCFGKI 353

Query: 361 TELSFPEGTS-RVDSGVRQGDTITPYYDPLIAKLIVHGQNRSAALGRLQDALKECRIGGT 419
           T    P G   R D+ +  G TI PYYD +  KL+V       AL R   AL + R+ G 
Sbjct: 354 TRYYAPGGPGVRTDTAIYTGYTIPPYYDSMCLKLVVWALTWEEALARGSRALDDMRVQGV 413

Query: 420 VTNRDFLIRLTEEHDFRSGHPDTGLIDREIERLTAPV--APGDEALALAAIFSTGA 473
            T   +  ++    DFRSG  +T  +D   E L   +   PG+ ALA+AA  +  A
Sbjct: 414 KTTATYYQQILANPDFRSGQFNTSFVDNHPELLNYSIKRKPGELALAIAAAIAAHA 469


Lambda     K      H
   0.319    0.135    0.394 

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: 776
Number of extensions: 45
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: 662
Length of database: 471
Length adjustment: 36
Effective length of query: 626
Effective length of database: 435
Effective search space:   272310
Effective search space used:   272310
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: 53 (25.0 bits)

This GapMind analysis is from Sep 17 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