GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Sinorhizobium meliloti 1021

Align Propionyl-CoA carboxylase, biotin carboxylase and biotin-carboxyl carrier subunit; PCC; EC 6.4.1.3; EC 6.3.4.14 (characterized)
to candidate SMc01345 SMc01345 acetyl-CoA carboxylase biotin carboxylase subunit

Query= SwissProt::I3R7G3
         (601 letters)



>FitnessBrowser__Smeli:SMc01345
          Length = 449

 Score =  424 bits (1091), Expect = e-123
 Identities = 210/444 (47%), Positives = 301/444 (67%), Gaps = 2/444 (0%)

Query: 1   MFSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSY 60
           M SK+L+ANRGEIA+RV+RAC+ELG+ TVAV+S AD    HVR ADE+  IGP  + +SY
Sbjct: 3   MISKILIANRGEIALRVLRACKELGIATVAVHSTADSDAMHVRLADESVCIGPPPSRESY 62

Query: 61  LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120
           L+   ++ A     ADA+HPGYGFL+ENA+FA  ++    T++GP+A+ +  +G+K  A+
Sbjct: 63  LNIHQIVAACEITGADAVHPGYGFLSENAKFADILDAHGITFIGPTAEHIRLMGDKITAK 122

Query: 121 SLMQDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQ 180
              ++  +PVVPG+       E+   +A   G+PV IKA  GGGGRG+KV  +E+E++  
Sbjct: 123 KTAEELGIPVVPGSDGEV-RPENALEIARQIGFPVLIKATAGGGGRGMKVARTEEELENA 181

Query: 181 FETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIE 240
             TA+ E  A F N +VY+EK+L  PRHIE+Q++ D  GN  HLGERDCSLQRRHQKV E
Sbjct: 182 VATARSEAAAAFGNDAVYMEKFLGKPRHIEIQVVGDGEGNAIHLGERDCSLQRRHQKVWE 241

Query: 241 EAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVEDGEFYFMEVNTRIQVEHTVTE 300
           EA SPAL+ + R +IG+     ++  +Y  AGT+EFL E+GEFYF+E+NTR+QVEH +TE
Sbjct: 242 EANSPALNVEQRMKIGQVCADAMKKLKYRGAGTIEFLYENGEFYFIEMNTRLQVEHPITE 301

Query: 301 EVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDPP 360
            +TG+D+V  Q+RVA+G  L   Q+D+   GH++E RINAE P + F P+ GT++ +  P
Sbjct: 302 AITGIDLVHEQIRVASGAGLSAKQEDIVFSGHAIECRINAEDP-RTFVPSPGTITHFHAP 360

Query: 361 GGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIPF 420
           GG+G+R+D    QG  I   YDS+I KLIV G  R E ++R  R L+EF I+G++T +P 
Sbjct: 361 GGLGVRVDSGAYQGYRIPPYYDSLIGKLIVHGRTRVECMMRLRRVLDEFVIDGIKTTLPL 420

Query: 421 HRLMLTDEAFREGSHTTKYLDEVL 444
            + ++ ++    G +   +L+  L
Sbjct: 421 FQDLINNQDIANGDYDIHWLEHHL 444


Lambda     K      H
   0.312    0.132    0.371 

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: 655
Number of extensions: 30
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: 601
Length of database: 449
Length adjustment: 35
Effective length of query: 566
Effective length of database: 414
Effective search space:   234324
Effective search space used:   234324
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 52 (24.6 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