GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pccA in Sinorhizobium meliloti 1021

Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate SM_b20756 SM_b20756 propionyl-CoA carboxylase subunit alpha

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



>lcl|FitnessBrowser__Smeli:SM_b20756 SM_b20756 propionyl-CoA
           carboxylase subunit alpha
          Length = 670

 Score =  932 bits (2410), Expect = 0.0
 Identities = 472/681 (69%), Positives = 544/681 (79%), Gaps = 14/681 (2%)

Query: 1   MFKKILIANRGEIACRVIKTARKMGIQTVAIYSDADRNALHVRMADEAVHIGPSPANQSY 60
           MFKKILIANRGEIACRVI+T + +GI TVA+YSDADR+A+HVRMADEAVHIGPSP++QSY
Sbjct: 4   MFKKILIANRGEIACRVIRTTKALGIPTVAVYSDADRDAMHVRMADEAVHIGPSPSSQSY 63

Query: 61  IVIDKVMDAIRQTGAEAVHPGYGFLSENKLFAEALEKEGVAFIGPPANAIEAMGDKITSK 120
           IVI+ ++ AIR+TGA+AVHPGYGFLSEN  FAEALEK+GV FIGPP  AIEAMGDKITSK
Sbjct: 64  IVIENILAAIRRTGADAVHPGYGFLSENAAFAEALEKDGVTFIGPPVRAIEAMGDKITSK 123

Query: 121 KIAQEANVSTVPGYMGLIADADEAVKISGEIGYPVMIKASAGGGGKGMRIAWNDAEAREG 180
           K+A EA V TVPG+MGLI DADEA +I+ EIG+PVMIKASAGGGGKGMRIAWN+ EAREG
Sbjct: 124 KLAAEAGVFTVPGHMGLIEDADEAARIAAEIGFPVMIKASAGGGGKGMRIAWNEREAREG 183

Query: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADTHGNCIYLGERECSIQRRNQKVVE 240
           FQSS+NEA +SFGDDRIFIEKFVT+PRHIEIQVL D HGN +YLGERECSIQRRNQKV+E
Sbjct: 184 FQSSRNEAKSSFGDDRIFIEKFVTEPRHIEIQVLGDKHGNILYLGERECSIQRRNQKVIE 243

Query: 241 EAPSPFLDEATRKAMGEQSCALAQAVGYASAGTVEFIVDGDRNFYFLEMNTRLQVEHPVT 300
           EAPSPFLDE TR+AMGEQ+ ALA+AVGY SAGTVEFIVD  RNFYFLEMNTRLQVEHPVT
Sbjct: 244 EAPSPFLDEKTRRAMGEQAVALAKAVGYHSAGTVEFIVDAGRNFYFLEMNTRLQVEHPVT 303

Query: 301 ELITGVDLVEQMIRVAAGEKLPMTQDDVTLTGWAIENRLYAEDPYRNFLPSIGRLTRYRP 360
           EL+TG+DLVEQMIRVAAG KL   Q DV L GWAIE+RLYAEDPYR FLPSIGRLTRYRP
Sbjct: 304 ELVTGLDLVEQMIRVAAGAKLAFAQKDVKLDGWAIESRLYAEDPYRTFLPSIGRLTRYRP 363

Query: 361 PVEVAAGPLEANGKWHGDAPSGPTAVRNDTGVYEGGEISMYYDPMIAKLCTWGPDRPAAI 420
           P E      +A+G          T +RNDTGV+EGGEISMYYDPMIAKLCTWGPDR  A+
Sbjct: 364 PEE----GTQADG----------TVIRNDTGVFEGGEISMYYDPMIAKLCTWGPDRLTAV 409

Query: 421 EAMRNALDGFEVEGIGHNLPFVAAVMDHPVFIKGEMTTAFIKEQYPDGFEGVTLGAADLT 480
            AM +ALD FEVEGIGHNLPF+AAVM    F +G +TTA+I E++  GF GV L  A   
Sbjct: 410 RAMADALDAFEVEGIGHNLPFLAAVMQQERFHEGRLTTAYIAEEFAGGFHGVALDDASAR 469

Query: 481 RLAAAAAAMFRVAEIRRTRISGTLDNHERMVGTDWVVTAQDARFDVTIDADPGGSTVRFA 540
           +LAA AA + +  + R +RISGT+ NH R+VG +WV +       VT +    G+ VRFA
Sbjct: 470 KLAAVAATVNQTLQERASRISGTIGNHRRVVGHEWVTSLDGHEIQVTCEVSADGTYVRFA 529

Query: 541 DGTAHRVTSRWTPGDSLATVEIDGAPMVLKVDKITSGFRMRFRGADVKVHVRTPRQAELN 600
           DGT+  V + W PG + A   ID  PM +KV+    G R+R+RG DV   VR+PR AEL 
Sbjct: 530 DGTSVSVATDWAPGRTRAAFNIDNQPMSVKVELAGPGIRLRWRGIDVVARVRSPRIAELA 589

Query: 601 DLMPEKLPPDTSKMLLCPMPGLVVKIDVEVGDEVQEGQALCTVEAMKMENILRAEKTATV 660
            LMP+KLPPDTSKMLLCPMPG+V  I V+ G+ V+ GQA+  VEAMKMENILRAEK A V
Sbjct: 590 RLMPKKLPPDTSKMLLCPMPGVVTSITVKAGETVEAGQAIAVVEAMKMENILRAEKRAIV 649

Query: 661 TKINAGAGDSLAVDDVIMEFE 681
            ++   AG SLAVD++IMEFE
Sbjct: 650 KRVAIEAGASLAVDELIMEFE 670


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: 1282
Number of extensions: 41
Number of successful extensions: 2
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: 670
Length adjustment: 39
Effective length of query: 642
Effective length of database: 631
Effective search space:   405102
Effective search space used:   405102
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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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