GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Shewanella oneidensis MR-1

Align propionyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.3) (characterized)
to candidate 201056 SO1894 acetyl-CoA carboxylase, biotin carboxylase, putative (NCBI ptt file)

Query= BRENDA::Q19842
         (724 letters)



>FitnessBrowser__MR1:201056
          Length = 694

 Score =  488 bits (1256), Expect = e-142
 Identities = 283/690 (41%), Positives = 417/690 (60%), Gaps = 29/690 (4%)

Query: 49  FDKILIANRGEIACRVIKTARAMGIKTVAVHSDVDSNSLHVKMADEAVCVGEAPTAKSYL 108
           F K+LIANRGEIACR+IKTA+AMG++TVA++SD D N+ HV MADE+  +G +  A SYL
Sbjct: 12  FTKLLIANRGEIACRIIKTAQAMGVRTVALYSDADKNARHVAMADESFYLGGSAPADSYL 71

Query: 109 RADRILQAVEDTGAQAVHPGYGFLSENTKFAAELEKAGAKFIGPNSKAILDMGDKIHSKK 168
           + D I+   +   AQA+HPGYGFLSEN  FA + E AG  F+GP S AI  MG K  +K 
Sbjct: 72  KGDLIIAIAKKAQAQAIHPGYGFLSENADFARKCEAAGIVFVGPGSDAIDAMGSKSAAKA 131

Query: 169 IATAARVSMIPGYDGEIADEDMCVKVSRDIGYPVMIKASAGGGGKGMRVAWNDKQAREGY 228
           I TAA+V ++PGY G+   +      +  IG+P++IKA+ GGGGKGMR+  ++ +  +  
Sbjct: 132 IMTAAQVPLVPGYHGDDQTDATLKAEALKIGFPMLIKAAYGGGGKGMRIVEHEGEIMDAI 191

Query: 229 RLSKQEAASSFGDDRMLVEKFIDNPRHIEMQVLCDKHGNALWLNERECSIQRRNQKVIEE 288
             +++EAASSFG+D++L+E+++  PRH+E+QV  D  GNA++L++R+CSIQRR+QKV+EE
Sbjct: 192 NSARREAASSFGNDKLLMERYLRQPRHVEVQVFADTFGNAIYLSDRDCSIQRRHQKVVEE 251

Query: 289 APSSFVPPEMRRKMGEQAVQLAKAVGYDSAGTVEFLVDSQRNFYFLEMNTRLQVEHPITE 348
           AP+  +  E+R +MGE AV  AKA+ Y  AGT+EFL+D+  +FYF+EMNTRLQVEHP+TE
Sbjct: 252 APAPGLSDELRAQMGEAAVAAAKAIDYVGAGTIEFLLDTDNSFYFMEMNTRLQVEHPVTE 311

Query: 349 CITGIDIVQQMLRVSYGHPLPITQEQVPLNGWAFESRVYAEDPYKGFGLPSVGRLSRYVE 408
            +TG D+V+  L V+ G PLP+ Q++V ++G AFE R+YAEDP   F LP+ G+L+   E
Sbjct: 312 MVTGQDLVKWQLMVASGQPLPLKQDEVRIHGHAFEVRIYAEDPQNEF-LPASGKLNFLRE 370

Query: 409 PKHVDGVRCDSGIREGSEISIYYDPLICKLVTHGDNREQALNRMQEALDNYVIRGVTHNI 468
           P+    VR DSGIRE   IS +YDP+I KL+   ++R +AL R+  AL++Y I G+ HNI
Sbjct: 371 PEQSKYVRIDSGIRENDVISNFYDPMIAKLIVWDESRPRALQRLVHALESYQISGLKHNI 430

Query: 469 PLLRDIVQEKRFRTGDITTKYLPEVYPEGFQGTSLSPKEQDVVIAFASALN--ARKLARA 526
             L +I +   F   D +T ++   Y +   G++ S  E D  +AFA+     ARK A  
Sbjct: 431 EFLANIAEHPAFAKADFSTDFINR-YGDALIGSASS--EADTALAFAALYQVLARKEAAK 487

Query: 527 NQFLNQNKQRST--HVASFSKTYKFVSSLPVKEGERPTEHAVEVEF---VEGSANKA--- 578
            Q +N     S    V+ F        S+ + +     +  V ++F    + S N++   
Sbjct: 488 AQAINSADPDSPWGQVSGFRLNSVSQHSIALLDDAHELQQLVLLDFGDHYQLSHNRSSQH 547

Query: 579 ----QVRIGGKTVTISGDLNLSHPVNSIEVDGEHITTQIVGKRAGEITVLYKGTPFKVKV 634
                   G  + ++SG+  L   +   E++G H +   V  +  + T+      +  + 
Sbjct: 548 QLSQSAADGQVSKSLSGE--LKQDLLLAEING-HKSKVPVSAQGDDFTLFLPSGSYHFRA 604

Query: 635 LPEQAVKYLQYMKEKAKVDLSTVVLSPMPGAIKNVNVKPGDMVSEGQELVVMEAMKMQNS 694
           +  Q V+     ++K K        +PM G +    V  G  V  GQ L+VMEAMKM+ +
Sbjct: 605 VKTQVVEAESSNEDKLK--------APMNGTVVTHLVDVGAEVKAGQGLLVMEAMKMEYT 656

Query: 695 LHAGKTGRVKAVNVKVGATVDEGEVLVELE 724
           + A   G V     K G  V +G VL+ +E
Sbjct: 657 IEAPFDGIVTEFYFKAGELVSDGAVLLHVE 686


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: 1100
Number of extensions: 42
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: 694
Length adjustment: 39
Effective length of query: 685
Effective length of database: 655
Effective search space:   448675
Effective search space used:   448675
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: 55 (25.8 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