GapMind for catabolism of small carbon sources

 

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

Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate WP_050656086.1 C1M55_RS09265 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

Query= reanno::Dino:3607308
         (681 letters)



>NCBI__GCF_002893965.1:WP_050656086.1
          Length = 679

 Score =  501 bits (1291), Expect = e-146
 Identities = 302/683 (44%), Positives = 406/683 (59%), Gaps = 48/683 (7%)

Query: 5   ILIANRGEIACRVIKTARKMGIQTVAIYSDADRNALHVRMADEAVHIGPSPANQSYIVID 64
           +L+ANRGEIA RVI+T R++GI++VA+YSDAD NA HVR AD AV+IGP+ A +SY+VID
Sbjct: 10  VLVANRGEIAVRVIRTLRELGIRSVAVYSDADANARHVREADTAVNIGPAAARESYLVID 69

Query: 65  KVMDAIRQTGAEAVHPGYGFLSENKLFAEALEKEGVAFIGPPANAIEAMGDKITSKKIAQ 124
           KV+DA + TGA+ +HPGYGFLSEN  F+ A    G+AF+GP  +AIE MGDKIT+K    
Sbjct: 70  KVIDAAKSTGAQGIHPGYGFLSENSAFSAACAAAGIAFLGPSEHAIEVMGDKITAKNSVA 129

Query: 125 EANVSTVPGYMGLIADADEAVKISGEIGYPVMIKASAGGGGKGMRIAWNDAEAREGFQSS 184
             +V  VPG        +E +  + +IGYPV++K SAGGGGKGMR+  + A   E  +S+
Sbjct: 130 AFDVPVVPGIARPNLTDEELIAAAEDIGYPVLVKPSAGGGGKGMRLVEDPANLAEALRSA 189

Query: 185 KNEAANSFGDDRIFIEKFVTQPRHIEIQVLADTHGNCIYLGERECSIQRRNQKVVEEAPS 244
           + EAA+SFGDD +F+E+FV +PRHIE+QVLAD HGN ++LGERECS+QRR+QKV+EEAPS
Sbjct: 190 RREAASSFGDDTLFLERFVLRPRHIEVQVLADQHGNVVHLGERECSLQRRHQKVIEEAPS 249

Query: 245 PFLDEATRKAMGEQSCALAQAVGYASAGTVEFIVDGDR--NFYFLEMNTRLQVEHPVTEL 302
           P LD+ TR  +G  +C  A++V Y  AGTVEFIV  D+   F+F+EMNTRLQVEHPVTE+
Sbjct: 250 PLLDQVTRDRIGAAACNTARSVDYTGAGTVEFIVSADKPDEFFFMEMNTRLQVEHPVTEM 309

Query: 303 ITGVDLVEQMIRVAAGEKLPMTQDDVTLTGWAIENRLYAEDPYRNFLPSIGRLTRYRPPV 362
           +TG+DLVE  +RVAAGEKL  +Q D+TLTG AIE R+YAEDP R FLP+ GR+      V
Sbjct: 310 VTGLDLVEWQVRVAAGEKLAFSQSDITLTGHAIEARVYAEDPGRGFLPTGGRV------V 363

Query: 363 EVAAGPLEANGKWHGDAPSGPTAVRNDTGVYEGGEISMYYDPMIAKLCTWGPDRPAAIEA 422
           ++               PSG + VR D+G+  G  +   YDPM++K+    PDR  A+  
Sbjct: 364 DLV-------------EPSG-SGVRVDSGLLAGTVVGSDYDPMLSKVIAHAPDRAGALRK 409

Query: 423 MRNALDGFEVEGIGHNLPFVAAVMDHPVFIKGEMTTAFIKEQYPDGFEGVTLGAADLTRL 482
           +  AL    V G+  N+ F   ++  P  I G + T  +  +  D        AAD +  
Sbjct: 410 LDRALGDTAVLGVVTNIEFARFLLADPDVIAGNLDTGLLDRRVED------FVAADASDE 463

Query: 483 AAAAAAMFRVAEIRRTRISGTLDNHERMVG--------TDWVVTAQDARFDVTIDADPGG 534
              AAA +R   + R   S   D  +   G        T   ++A      V I   P  
Sbjct: 464 VLIAAAAYR--WLSRWTTSERFDPWDVPSGWRVGTPAPTSIRLSAGTRTAHVAIVGVPAA 521

Query: 535 STVRFADGTAHRVTSRWTPGDSLATVEIDGAPMVLKVDKITSGFRMRFRGADVKVHVRTP 594
           + V   +G+  R  S    G  LA V IDG      V +   G  +   G     HVR  
Sbjct: 522 AKVE-VEGSQPRAFSATLTGSELAVV-IDGRRRTFVVAETDGGLWLAGGGT---WHVR-- 574

Query: 595 RQAELNDLMPEKLPPDTSKMLLCPMPGLVVKIDVEVGDEVQEGQALCTVEAMKMENILRA 654
             AE++    +K   D    +  PMPG V+ ++VE G  V  GQ L  VEAMKME+ L +
Sbjct: 575 EVAEVSVRGEDKHAGDAE--IASPMPGAVIAVNVENGAAVSAGQPLVVVEAMKMEHSLTS 632

Query: 655 EKTATVTKINAGAGDSLAVDDVI 677
                + ++    GD + VD V+
Sbjct: 633 PIDG-IVEVLVRQGDQVMVDQVL 654


Lambda     K      H
   0.318    0.134    0.392 

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: 1146
Number of extensions: 51
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: 681
Length of database: 679
Length adjustment: 39
Effective length of query: 642
Effective length of database: 640
Effective search space:   410880
Effective search space used:   410880
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 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