GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Azospirillum thiophilum BV-S

Align Propionyl-CoA carboxylase alpha chain; EC 6.4.1.3 (characterized)
to candidate WP_045585974.1 AL072_RS28295 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

Query= SwissProt::Q5LUF3
         (681 letters)



>NCBI__GCF_001305595.1:WP_045585974.1
          Length = 667

 Score =  541 bits (1393), Expect = e-158
 Identities = 319/693 (46%), Positives = 418/693 (60%), Gaps = 44/693 (6%)

Query: 1   MFNKILIANRGEIACRVIKTARKMGISTVAIYSDADKQALHVQMADEAVHIGPPPANQSY 60
           MF+KILIANRGEIACRVI+TAR+MGI TVA++S+AD  A+HVQMADEAV IGP P  +SY
Sbjct: 1   MFDKILIANRGEIACRVIRTARRMGIRTVAVHSEADAHAMHVQMADEAVCIGPAPVGESY 60

Query: 61  IVIDKVMAAIRATGAQAVHPGYGFLSENSKFAEALEAEGVIFVGPPKGAIEAMGDKITSK 120
           +  D ++   R TGAQA+HPGYGFLSEN+ FA A  A GV+F+GPP  AI  MG K  SK
Sbjct: 61  LRGDVILDVARRTGAQAIHPGYGFLSENAGFAAACAAAGVVFIGPPIDAIRVMGSKAESK 120

Query: 121 KIAQEANVSTVPGYMGLIEDADEAVKISNQIGYPVMIKASAGGGGKGMRIAWNDQEAREG 180
           ++   A+V  VPGY G  +D       + +IGYPV++KASAGGGGKGMR+     E  + 
Sbjct: 121 RLMANADVPLVPGYHGTDQDFATLSAEAERIGYPVLVKASAGGGGKGMRVVRAAAELADA 180

Query: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLCDSHGNGIYLGERECSIQRRNQKVVE 240
              ++ EA  +FGDD + +EK++++PRH+EIQV CD+HGNG+YL ER+CS+QRR+QKV+E
Sbjct: 181 VAGAQREAKAAFGDDSLLLEKYLSRPRHVEIQVFCDTHGNGVYLFERDCSVQRRHQKVIE 240

Query: 241 EAPSPFLDEATRRAMGEQAVALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVT 300
           EAP+P L +  RR MGE AVA AKAV Y  AGTVEF+ +    FYF+EMNTRLQVEHPVT
Sbjct: 241 EAPAPNLPDDLRRRMGEAAVAAAKAVSYVGAGTVEFLYE-DGGFYFIEMNTRLQVEHPVT 299

Query: 301 ELITGVDLVEQMIRVAAGEPLSITQGDVKLTGWAIENRLYAEDPYRGFLPSIGRLTRYRP 360
           E ITG+DLVE  +RVA+G  L + Q  +   G A E RLYAEDP R FLP+IGRL R RP
Sbjct: 300 EKITGLDLVEWQLRVASGAELPLRQDQLTRRGHAFEARLYAEDPQRDFLPAIGRLLRLRP 359

Query: 361 PAETAAGPLLVNGKWQGDAPSGEAAVRNDTGVYEGGEISMYYDPMIAKLCTWAPTRAAAI 420
           PAET                     VR DTGV EG  ++MYYDPMIAKL  W   R +A+
Sbjct: 360 PAET-------------------EHVRVDTGVREGDSVTMYYDPMIAKLIVWDEDRDSAL 400

Query: 421 EAMRIALDSFEVEGIGHNLPFLSAVMDHPKFISGDMTTAFIAEEYPEGFEGVNLPETDLR 480
             +R+AL  +EV G+  N+ FL A+  HP F + ++ T FI E +         P  D  
Sbjct: 401 RRLRVALAEYEVVGVTTNVAFLGAIAGHPAFRAVEIDTGFI-ERHRADLLPPPAPVADRA 459

Query: 481 RVAAAAAAMHRVAEIRRTRVSGRMDNHER-------RVGTEWVVTLQGAD----FPVTIA 529
             AA+ + + +  E  +  +  R D H         R+  E    L+  D      VT+ 
Sbjct: 460 LAAASLSVLLKRREEAQAALRARSDRHSPWLLANGWRLNEENHYDLRLMDGETAREVTLH 519

Query: 530 ADHDGSTVSFDDGSSMRVTS-DWTPGDQLANLMVDGAPLVLKVGKISGGFRIRTRGADLK 588
              D   V+ D G  M VT    T G   A L  DG      V +      +   GA  +
Sbjct: 520 FRGDDYEVAVDGGKPMPVTGVSLTDGVLTATL--DGMRTRATVVRQGLDLTVLIDGAVSR 577

Query: 589 VHVRTPRQAELARLMPEKLPPDTSKMLLCPMPGLIVKVDVEVGQEVQEGQALCTIEAMKM 648
           + +  P     AR   ++     S  L  PMPG +V+V VE GQ V+ G  L  +EAMKM
Sbjct: 578 LTLDDPS----ARAAEQE---GGSGRLTAPMPGTVVRVLVEPGQSVEAGTPLMLLEAMKM 630

Query: 649 ENILRAEKKGVVAKINASAGNSLA--VDDVIME 679
           E+ ++A   G V+ +N SAG+ ++  VD ++++
Sbjct: 631 EHTIKAPAAGTVSAVNFSAGDQVSEGVDLLVLD 663


Lambda     K      H
   0.317    0.134    0.387 

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: 1162
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: 667
Length adjustment: 39
Effective length of query: 642
Effective length of database: 628
Effective search space:   403176
Effective search space used:   403176
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.

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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:

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