GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Shewanella sp. ANA-3

Align propionyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.3) (characterized)
to candidate 7024491 Shewana3_1669 3-methylcrotonoyl-CoA carboxylase, alpha subunit (RefSeq)

Query= BRENDA::Q19842
         (724 letters)



>FitnessBrowser__ANA3:7024491
          Length = 674

 Score =  492 bits (1266), Expect = e-143
 Identities = 280/678 (41%), Positives = 412/678 (60%), Gaps = 19/678 (2%)

Query: 51  KILIANRGEIACRVIKTARAMGIKTVAVHSDVDSNSLHVKMADEAVCVGEAPTAKSYLRA 110
           K+LIANRGEIACR+IKTA+AMG++TVA++SD D N+ HV MADE+  +G +  A SYL+ 
Sbjct: 4   KLLIANRGEIACRIIKTAQAMGVRTVALYSDADKNARHVAMADESFYLGGSAPADSYLKG 63

Query: 111 DRILQAVEDTGAQAVHPGYGFLSENTKFAAELEKAGAKFIGPNSKAILDMGDKIHSKKIA 170
           D I++  +   AQA+HPGYGFLSEN  FA + E AG  F+GP S AI  MG K  +K I 
Sbjct: 64  DLIIEIAKKAQAQAIHPGYGFLSENADFARKCEAAGIVFVGPGSDAIDAMGSKSAAKAIM 123

Query: 171 TAARVSMIPGYDGEIADEDMCVKVSRDIGYPVMIKASAGGGGKGMRVAWNDKQAREGYRL 230
           TAA+V ++PGY G+   +      +  IG+P++IKA+ GGGGKGMR+  ++ +  +    
Sbjct: 124 TAAQVPLVPGYHGDDQTDATLKAEALKIGFPMLIKAAYGGGGKGMRIVEHEGEIMDAINS 183

Query: 231 SKQEAASSFGDDRMLVEKFIDNPRHIEMQVLCDKHGNALWLNERECSIQRRNQKVIEEAP 290
           +++EAASSFG+D++L+E+++  PRH+E+QV  D  GNA++L++R+CSIQRR+QKV+EEAP
Sbjct: 184 ARREAASSFGNDKLLMERYLRQPRHVEVQVFADTFGNAIYLSDRDCSIQRRHQKVVEEAP 243

Query: 291 SSFVPPEMRRKMGEQAVQLAKAVGYDSAGTVEFLVDSQRNFYFLEMNTRLQVEHPITECI 350
           +  +  E+R +MGE AV  AKA+ Y  AGTVEFL+D+  +FYF+EMNTRLQVEHP+TE +
Sbjct: 244 APGLSDELRTQMGEAAVAAAKAIDYVGAGTVEFLLDTDNSFYFMEMNTRLQVEHPVTEMV 303

Query: 351 TGIDIVQQMLRVSYGHPLPITQEQVPLNGWAFESRVYAEDPYKGFGLPSVGRLSRYVEPK 410
           TG D+V+  L V+ G PLP+ Q++V ++G AFE R+YAEDP   F LP+ G+L+   EP+
Sbjct: 304 TGQDLVKWQLMVASGQPLPLKQDEVRIHGHAFEVRIYAEDPQNEF-LPASGKLNFLREPE 362

Query: 411 HVDGVRCDSGIREGSEISIYYDPLICKLVTHGDNREQALNRMQEALDNYVIRGVTHNIPL 470
               VR DSGIRE   IS +YDP+I KL+   ++R +AL R+  AL++Y I G+ HNI  
Sbjct: 363 QSKYVRIDSGIRENDVISNFYDPMIAKLIVWDESRPRALQRLVHALESYQISGLKHNIEF 422

Query: 471 LRDIVQEKRFRTGDITTKYLPEVYPEGFQGTSLSPKEQDVVIAFASALN--ARKLARANQ 528
           L +I +   F   D +T ++      G    S +  E D  +AFA+     ARK A   Q
Sbjct: 423 LANIAEHPAFAKADFSTDFINRY---GDALISSASSETDTALAFAALYQVLARKEAAKAQ 479

Query: 529 FLNQNKQRST--HVASFSKTYKFVSSLPVKEGERPTEHAVEVEFVEGSANKAQVRIGGKT 586
            +N     S    V+ F        S+ + +     +  V ++F +          G  +
Sbjct: 480 AINSADPYSPWGQVSGFRLNSVSQHSIALLDDAHELQQLVLLDFGDHYQLSQPTADGQVS 539

Query: 587 VTISGDLNLSHPVNSIEVDGEHITTQIVGKRAGEITVLYKGTPFKVKVLPEQAVKYLQYM 646
            ++SG+  L   +   E++G H +   V  +  + T+      +  + +  Q V+     
Sbjct: 540 KSLSGE--LKQDLLLAEING-HKSKVPVSAQGDDFTLFLPSGSYHFRAVKTQVVEAESSN 596

Query: 647 KEKAKVDLSTVVLSPMPGAIKNVNVKPGDMVSEGQELVVMEAMKMQNSLHAGKTGRVKAV 706
           ++K K        +PM G +    V+ G  V+ GQ L+VMEAMKM+ ++ A   G V   
Sbjct: 597 EDKLK--------APMNGTVVTHLVEVGAEVNAGQGLLVMEAMKMEYTIEAPFDGIVTEF 648

Query: 707 NVKVGATVDEGEVLVELE 724
             K G  V +G VL+ +E
Sbjct: 649 YFKAGELVSDGAVLLHVE 666


Lambda     K      H
   0.316    0.133    0.378 

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: 1091
Number of extensions: 44
Number of successful extensions: 3
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: 724
Length of database: 674
Length adjustment: 39
Effective length of query: 685
Effective length of database: 635
Effective search space:   434975
Effective search space used:   434975
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 (21.6 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