Alignments for a candidate for pccA in Marinobacter adhaerens HP15

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 GFF1023 HP15_1002 methylcrotonyl-CoA carboxylase, alpha subunit

Query= SwissProt::Q5LUF3
         (681 letters)



>FitnessBrowser__Marino:GFF1023
          Length = 664

 Score =  497 bits (1280), 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 LAAAKREAQNAFGNPDMLIERYLTQPRHVEIQVFCDQDGKGVYLAERDCSVQRRHQKVLE 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--VINGHRISIHGNLHNDQLM 563

Query: 593 TPRQAELARLMPEKLPPDTSKM-----LLCPMPGLIVKVDVEVGQEVQEGQALCTIEAMK 647
              + +       K      +M     L  PM G IV V  +VG +V  GQ+L  +EAMK
Sbjct: 564 LFYEGDTFNCTVYKESYGFEEMASEGSLAAPMNGAIVAVQAKVGDKVTAGQSLVIMEAMK 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: 49
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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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources