GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Smeli:SM_b20756
          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.

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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