Alignments for a candidate for liuB in Rhodococcus qingshengii djl-6-2

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuB in Rhodococcus qingshengii djl-6-2

Align methylcrotonoyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.4) (characterized)
to candidate WP_050656406.1 C1M55_RS08885 acetyl-CoA carboxylase subunit alpha

Query= BRENDA::Q9I299
         (655 letters)



>NCBI__GCF_002893965.1:WP_050656406.1
          Length = 661

 Score =  483 bits (1242), Expect = e-140
 Identities = 308/681 (45%), Positives = 405/681 (59%), Gaps = 63/681 (9%)

Query: 7   SIQRLLVANRGEIACRVMRSARALGIGSVAVHSDIDRHARHVAEADIAVDLGGAKPADSY 66
           +I  +LVANRGEIA RV  + R  GIG+VAV SD D  + HVAEAD +V L G  PA++Y
Sbjct: 2   TITSVLVANRGEIARRVFATCRKNGIGTVAVFSDADADSPHVAEADASVRLPGNTPAETY 61

Query: 67  LRGDRIIAAALASGAQAIHPGYGFLSENADFARACEEAGLLFLGPPAAAIDAMGSKSAAK 126
           LRG+ +IAAA ASGA AIHPGYGFLSENA+FAR+  +AGL ++GPP  +I+ MGSK  +K
Sbjct: 62  LRGELVIAAAKASGADAIHPGYGFLSENAEFARSVIDAGLTWIGPPVESIELMGSKVESK 121

Query: 127 ALMEEAGVPLVPGYHGEAQDLETFRREAGRIGYPVLLKAAAGGGGKGMKVVEREAELAEA 186
            +M+ AGVP++          E           PVL+KA+AGGGG+GM+VV   + L   
Sbjct: 122 KIMDAAGVPVLS---------ELDPAAVTEAHLPVLIKASAGGGGRGMRVVRELSALDGE 172

Query: 187 LSSAQREAKAAFGDARMLVEKYLLKPRHVEIQVFADRHGHCLYLNERDCSIQRRHQKVVE 246
           L +A+REA++AFGD  +  E+YL   RH+E+QV ADRHG    + ER+CSIQRRHQKVVE
Sbjct: 173 LEAARREAQSAFGDPTVFCERYLETGRHIEVQVMADRHGAVWAVGERECSIQRRHQKVVE 232

Query: 247 EAPAPGLG--AELRRAMGEAAVRAAQAIGYVGAGTVEFLLDERGQFFFMEMNTRLQVEHP 304
           EAP+P +     +R  + +A+  AA AIGY GAGTVEFL DE+G FFF+EMNTRLQVEHP
Sbjct: 233 EAPSPLVQRIPAMRDKLFDASRLAANAIGYEGAGTVEFLADEKGDFFFLEMNTRLQVEHP 292

Query: 305 VTEAITGLDLVAWQIRVARGEALPLTQEQVPLNGHAIEVRLYAEDPEGDFLPASGRLMLY 364
           VTE  TGLDLV  Q++VA GEALP   +Q  + GH+IEVRLYAEDP  ++ P SG +  +
Sbjct: 293 VTECTTGLDLVELQLQVASGEALP--DDQPEIRGHSIEVRLYAEDPAKNWQPQSGTVH-H 349

Query: 365 REAAAGP---------GRRVDSGVREGDEVSPFYDPMLAKLIAWGETREEARQRLLAMLA 415
            E    P         G R+DSGV +G  V   YDPMLAK+I++  TR  A + L + LA
Sbjct: 350 IELPGDPQEFSVLREQGVRLDSGVVDGSVVGVHYDPMLAKVISYAPTRTAAARLLASTLA 409

Query: 416 ETSVGGLRTNLAFLRRILGHPAFAAAELDTGFIARHQDDLLPAPQALPEHFWQAAAEAWL 475
            T + GLRTN   L  +L HPAF A + DT F   H  + L  P A  +    +A  A L
Sbjct: 410 RTRIHGLRTNRDLLVNVLAHPAFIAGDTDTAFFETHDLEKLSTPLADTDAERLSALAAAL 469

Query: 476 QSEPGHRRDDD-------------PHSPWSRNDGW-------RSALARESDLMLRCRDER 515
            ++  H R                P  P S++          R +L+R   L     D+ 
Sbjct: 470 -ADAAHNRASARVIGRLPSGWRNLPSQPQSKSYSTASGDYDVRYSLSRSGVLSAEGFDD- 527

Query: 516 RCVRLRHASPSQYRLDGDDLVSRVDGVTRRSAALRRGRQLFLEWEGELLAIEA----VDP 571
             VRL  A+ ++       +V    GV R       G ++F++     +A+ A    VDP
Sbjct: 528 --VRLVSATATR-------VVLEQSGVQRSFDVAAYGSEIFVDSSLGPVALTAAPRFVDP 578

Query: 572 IAEAEAAHAHQGGLSAPMNGSIVRVLVEPGQTVEAGATLVVLEAMKMEHSIRAPHAGVVK 631
            AE  A     G L APM GS++R+    G TV AG  ++ LEAMKMEH++ AP AGV+ 
Sbjct: 579 SAEVAA-----GSLLAPMPGSVIRLGAALGDTVTAGQPILWLEAMKMEHTVTAPTAGVLV 633

Query: 632 ALYCSEGELVEEGTPLVELDE 652
            L  + G+ VE G+ L  ++E
Sbjct: 634 ELPVAVGQQVEVGSVLARVEE 654


Lambda     K      H
   0.319    0.135    0.397 

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: 1006
Number of extensions: 48
Number of successful extensions: 7
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: 655
Length of database: 661
Length adjustment: 38
Effective length of query: 617
Effective length of database: 623
Effective search space:   384391
Effective search space used:   384391
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: 54 (25.4 bits)

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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 2024 update 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