GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Marinobacter adhaerens HP15

Align Propionyl-CoA carboxylase alpha chain; EC 6.4.1.3 (characterized)
to candidate GFF4239 HP15_4179 methylcrotonyl-CoA carboxylase, alpha subunit

Query= SwissProt::Q5LUF3
         (681 letters)



>FitnessBrowser__Marino:GFF4239
          Length = 664

 Score =  497 bits (1279), Expect = e-145
 Identities = 291/685 (42%), Positives = 403/685 (58%), Gaps = 50/685 (7%)

Query: 1   MFNKILIANRGEIACRVIKTARKMGISTVAIYSDADKQALHVQMADEAVHIGPPPANQSY 60
           MF+KILIANRGEIACR+I+TA +MGI  VA+YS+AD  A HV MADEA HIGP P+++SY
Sbjct: 1   MFSKILIANRGEIACRIIQTAHRMGIRVVAVYSEADANARHVAMADEAFHIGPAPSSESY 60

Query: 61  IVIDKVMAAIRATGAQAVHPGYGFLSENSKFAEALEAEGVIFVGPPKGAIEAMGDKITSK 120
           +  +K++   + +GAQA+HPGYGFLSEN+ FAE+ EA  ++F+GPP  AI AMG K  +K
Sbjct: 61  LRAEKIIEIAKKSGAQAIHPGYGFLSENTGFAESCEANNIVFIGPPSSAIAAMGSKSAAK 120

Query: 121 KIAQEANVSTVPGYMGLIEDADEAVKISNQIGYPVMIKASAGGGGKGMRIAWNDQEAREG 180
            I ++A V  VPGY G  +  +     + + G+P+++KA AGGGGKGMR+  N  E  + 
Sbjct: 121 AIMEKAGVPLVPGYHGDDQSVETLRAEAEKCGFPLLLKAVAGGGGKGMRVVNNMGEFDDA 180

Query: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLCDSHGNGIYLGERECSIQRRNQKVVE 240
             ++K EA N+FG+  + IE+++TQPRH+EIQV CD  G G+YL ER+CS+QRR+QKV+E
Sbjct: 181 LAAAKREAQNAFGNPDMLIERYLTQPRHVEIQVFCDQEGKGVYLAERDCSVQRRHQKVLE 240

Query: 241 EAPSPFLDEATRRAMGEQAVALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVT 300
           EAP+P L E TR+AMGE AV  A+A+ Y  AGTVEF+ D   +F+F+EMNTRLQVEHPVT
Sbjct: 241 EAPAPGLSEETRKAMGEAAVRAAQAINYVGAGTVEFLYDVDGSFFFMEMNTRLQVEHPVT 300

Query: 301 ELITGVDLVEQMIRVAAGEPLSITQGDVKLTGWAIENRLYAEDPYRGFLPSIGRLTRYRP 360
           E++TG DLVE  ++VA G+ L + Q  VK  G A+E R+YAEDP + FLP+ G L     
Sbjct: 301 EMVTGQDLVEWQLKVAWGDALPLEQSQVKTRGHALEARIYAEDPDQDFLPATGNLRYLST 360

Query: 361 PAETAAGPLLVNGKWQGDAPSGEAAVRNDTGVYEGGEISMYYDPMIAKLCTWAPTRAAAI 420
           P E+                   A VR DTGV EG +IS++YDPMIAKL  W  TR  AI
Sbjct: 361 PDES-------------------AHVRVDTGVTEGDDISIHYDPMIAKLIVWDETRDQAI 401

Query: 421 EAMRIALDSFEVEGIGHNLPFLSAVMDHPKFISGDMTTAFIAEEYPEGFEGVNLPETDLR 480
             M  AL+ + + G+  N+ FL A+ D   F   ++TT FI     +    +  P++ L 
Sbjct: 402 NRMVQALEHYRIAGVKTNIRFLHALADAQPFREAELTTGFI-----DDHRELLFPKSKLD 456

Query: 481 RVAAAAAAMHRVAEIRRTRVSGRMD-------NHERRVGTEWVVTLQGADFPVTIAAD-H 532
              A   A   V E R++R     D        +  R+ +E+   LQ     + +  + H
Sbjct: 457 THKALVLAAGFVLEQRKSREVVSTDPWSPFGRQNSWRMNSEFAQPLQ-----LQVGEEIH 511

Query: 533 DGSTVSFDDGSSMRVTSDWTPGDQLANLMVDGAPLVLKVGKISGGFRIRTRGADLKVHVR 592
           D   +  DD   + V      GD + NL        L+   +  G RI   G      + 
Sbjct: 512 DLKVLERDDRYQVFV------GDSVYNLTARLDDDYLQA--VINGHRISIHGNLHNDQLV 563

Query: 593 TPRQAELARLMPEKLPPDTSKM-----LLCPMPGLIVKVDVEVGQEVQEGQALCTIEAMK 647
              + +       K      +M     L  PM G IV V  +VG +V  GQ+L  +EAMK
Sbjct: 564 LFYEGDTFNCTVYKESYGFEEMAGEGSLAAPMNGAIVAVQAKVGDKVTAGQSLVIMEAMK 623

Query: 648 MENILRAEKKGVVAKINASAGNSLA 672
           ME+ ++A   GVV +I  + G+ ++
Sbjct: 624 MEHAIKAPADGVVTEIFFAEGDQVS 648


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: 1075
Number of extensions: 51
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 681
Length of database: 664
Length adjustment: 39
Effective length of query: 642
Effective length of database: 625
Effective search space:   401250
Effective search space used:   401250
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