GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Caulobacter crescentus NA1000

Align Propionyl-CoA carboxylase alpha chain; EC 6.4.1.3 (characterized)
to candidate CCNA_02261 CCNA_02261 propionyl-CoA carboxylase biotin-containing subunit

Query= SwissProt::Q5LUF3
         (681 letters)



>FitnessBrowser__Caulo:CCNA_02261
          Length = 669

 Score =  768 bits (1984), Expect = 0.0
 Identities = 395/682 (57%), Positives = 486/682 (71%), Gaps = 16/682 (2%)

Query: 1   MFNKILIANRGEIACRVIKTARKMGISTVAIYSDADKQALHVQMADEAVHIGPPPANQSY 60
           MF+KILIANRGEIA RVIKT R++GI TV +YSDAD  +L V+MADE VHIG  PANQSY
Sbjct: 1   MFSKILIANRGEIAVRVIKTCRRLGIKTVVVYSDADAGSLAVEMADETVHIGASPANQSY 60

Query: 61  IVIDKVMAAIRATGAQAVHPGYGFLSENSKFAEALEAEGVIFVGPPKGAIEAMGDKITSK 120
           +V DK++AA + TGAQAVHPG+GFLSEN+ FA+    EG++F+GP  GAI AMGDKI SK
Sbjct: 61  LVADKIIAACKQTGAQAVHPGFGFLSENAGFAQRCADEGIVFIGPNPGAISAMGDKIESK 120

Query: 121 KIAQEANVSTVPGYMGLIEDADEAVKISNQIGYPVMIKASAGGGGKGMRIAWNDQEAREG 180
           K AQ A VS VPG++G I D  EAVKIS +IGYPVMIKASAGGGGKG+R+AW  ++  EG
Sbjct: 121 KFAQAAGVSCVPGHIGEIADTAEAVKISEEIGYPVMIKASAGGGGKGIRVAWTRKDVEEG 180

Query: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLCDSHGNGIYLGERECSIQRRNQKVVE 240
           F + + EA  SFGDDRIFIEKF+  PRHIEIQVL D HGN ++L ERECSIQRRNQKV+E
Sbjct: 181 FPAVRAEAKASFGDDRIFIEKFIESPRHIEIQVLGDKHGNVVHLFERECSIQRRNQKVIE 240

Query: 241 EAPSPFLDEATRRAMGEQAVALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVT 300
           EAPSP LDEATR AMG QAVALAKAV Y SAGTVEF+    K+F+FLEMNTRLQVEHPVT
Sbjct: 241 EAPSPLLDEATRNAMGAQAVALAKAVNYDSAGTVEFVAGQDKSFFFLEMNTRLQVEHPVT 300

Query: 301 ELITGVDLVEQMIRVAAGEPLSITQGDVKLTGWAIENRLYAEDPYRGFLPSIGRLTRYRP 360
           ELITG+DLVEQMIR A GE ++  Q D+ + GWAIE+R+YAEDPYR FLPSIGRL RY P
Sbjct: 301 ELITGLDLVEQMIRSAYGEKMAFGQSDLSINGWAIESRIYAEDPYRKFLPSIGRLVRYDP 360

Query: 361 PAETAAGPLLVNGKWQGDAPSGEAAVRNDTGVYEGGEISMYYDPMIAKLCTWAPTRAAAI 420
           PAE              D P+G   VRND GV EG EISM+YDPMI+KLCTWAPTR AAI
Sbjct: 361 PAE-----------GDKDGPNGGYVVRNDAGVREGDEISMFYDPMISKLCTWAPTRLAAI 409

Query: 421 EAMRIALDSFEVEGIGHNLPFLSAVMDHPKFISGDMTTAFIAEEYPEGFEGVNLPETDLR 480
           + M  AL+ F +EG+G N+PFL+AVMD  +F SG + T++I +E+P+GF G       L 
Sbjct: 410 DGMGRALEDFHIEGLGQNIPFLAAVMDEERFRSGKLATSYIKDEFPDGFNGTTPTAVQLD 469

Query: 481 RVAAAAAAMHRVAEIRRTRVSGRMDNHERRVGTEWVVTLQGADFPVTIAADHDGSTVS-F 539
            + A  AAM RV   R       +    R    EWVV +      V +  +     V   
Sbjct: 470 ILTAVGAAMQRVYATRARSYESGLIGEAR---DEWVVAIGETRLRVKVGGEDGAVAVELL 526

Query: 540 DDGSSMRVTS-DWTPGDQLANLMVDGAPLVLKVGKISGGFRIRTRGADLKVHVRTPRQAE 598
           D+G ++ +T  DW PG  +   +++G    ++    + GF IR R A  +V V TPR AE
Sbjct: 527 DEGRTLFLTDIDWRPGKPVFKAVLNGLAFTVQAAPAAEGFTIRHRAAKTRVLVLTPRSAE 586

Query: 599 LARLMPEKLPPDTSKMLLCPMPGLIVKVDVEVGQEVQEGQALCTIEAMKMENILRAEKKG 658
           L   +PEK   DTSK++L PMPGL+V +DV  GQ+V+EG+ +C +EAMKM+NI+RAE+ G
Sbjct: 587 LHDKLPEKQAADTSKLVLSPMPGLVVSMDVTTGQQVREGEVVCVLEAMKMQNIIRAERDG 646

Query: 659 VVAKINASAGNSLAVDDVIMEF 680
           VV  +NA  G+ +A D+V++EF
Sbjct: 647 VVKAVNAKGGDPVAADEVLVEF 668


Lambda     K      H
   0.317    0.134    0.387 

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: 1175
Number of extensions: 48
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: 681
Length of database: 669
Length adjustment: 39
Effective length of query: 642
Effective length of database: 630
Effective search space:   404460
Effective search space used:   404460
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