Alignments for a candidate for pccA in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA in Halomonas desiderata SP1

Align Propionyl-CoA carboxylase alpha chain; EC 6.4.1.3 (characterized)
to candidate WP_086510401.1 BZY95_RS13285 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha

Query= SwissProt::Q5LUF3
         (681 letters)



>NCBI__GCF_002151265.1:WP_086510401.1
          Length = 681

 Score =  501 bits (1291), Expect = e-146
 Identities = 296/697 (42%), Positives = 408/697 (58%), Gaps = 48/697 (6%)

Query: 2   FNKILIANRGEIACRVIKTARKMGISTVAIYSDADKQALHVQMADEAVHIGPPPANQSYI 61
           F+ +L+ANRGEIACRV++TAR MG+ TVA+YSDAD  A HV+ ADEAV +GP  A +SY+
Sbjct: 11  FDTLLVANRGEIACRVMRTARAMGLRTVAVYSDADANARHVREADEAVRLGPAAARESYL 70

Query: 62  VIDKVMAAIRATGAQAVHPGYGFLSENSKFAEALEAEGVIFVGPPKGAIEAMGDKITSKK 121
            ++ V+ A + TGA A+HPGYGFLSEN  F +AL+A G+ FVGPP  AI AMGDK  +K 
Sbjct: 71  KVEAVVEAAKRTGAGAIHPGYGFLSENGAFVQALDAAGITFVGPPASAIAAMGDKSAAKA 130

Query: 122 IAQEANVSTVPGYMGLIEDADEAVKIS--NQIGYPVMIKASAGGGGKGMRIAWNDQEARE 179
               A V  VPGY G  +D D+A+  S  ++IGYPV++KASAGGGGKGMR+    ++ + 
Sbjct: 131 RMANAGVPLVPGYHG--DDQDDALLKSEADKIGYPVLLKASAGGGGKGMRVVEAPEQFQA 188

Query: 180 GFQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLCDSHGNGIYLGERECSIQRRNQKVV 239
                + E+  +FGD R+ IEK++TQPRH+E+QV CDSHGNG+YL ER+CS+QRR+QKV+
Sbjct: 189 ALDGCRRESQAAFGDTRMLIEKYLTQPRHVEVQVFCDSHGNGVYLFERDCSVQRRHQKVL 248

Query: 240 EEAPSPFLDEATRRAMGEQAVALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPV 299
           EEAP+P +    RR MGE AV  AK +GY  AGTVEF++D   +FYF+EMNTRLQVEHPV
Sbjct: 249 EEAPAPGMTAELRREMGEAAVRAAKEIGYVGAGTVEFLLDKDGSFYFMEMNTRLQVEHPV 308

Query: 300 TELITGVDLVEQMIRVAAGEPLSITQGDVKLTGWAIENRLYAEDPYRGFLPSIGRLTRYR 359
           TE+ITG DLVE  +RVA GE L + Q ++ +TG + E RLYAEDP + FLP+ GRL R+ 
Sbjct: 309 TEMITGQDLVEWQLRVAMGETLPLQQEELTITGHSFEARLYAEDPEQDFLPATGRLERF- 367

Query: 360 PPAETAAGPLLVNGKWQGDAPSGEAAVRNDTGVYEGGEISMYYDPMIAKLCTWAPTRAAA 419
                      ++ K  G  P     VR D+GV  G  +SM+YDPM+AKL      R  A
Sbjct: 368 ----------AMDLKGAGLDP---RQVRLDSGVETGDVVSMHYDPMLAKLIVHGDDRDQA 414

Query: 420 IEAMRIALDSFEVEGIGHNLPFLSAVMDHPKFISGDMTTAFIAEEYPEGFEGVNLPETDL 479
           +  +  AL + +V+G+  N  FL  +  HP F + ++ T FI +     F     P+   
Sbjct: 415 LSTLNRALAALDVQGVVTNRAFLQRLATHPAFRNAELDTRFIEKNEATLF----APKQYS 470

Query: 480 RRVAAAAAAMHRVAEIRRTRVSGRMDNHER-RVGTEWVVTLQGADFPVTIAADHDGSTVS 538
               A AA +      R        D H+  R+     + +   D   +IA  HD   V 
Sbjct: 471 IEEYAGAALIGLNQLARECESDSPWDRHDGFRLNAPHTIRISLCD--PSIAQVHDAEGVV 528

Query: 539 FDDGSSMRVTSDWTPGDQLANLMVDGAPLVLKVGKISG--------GFRIRTRG-ADLKV 589
             +G+       W       +L + G  L  ++  + G        G R R +   D  V
Sbjct: 529 VVEGTRASGADPW-------DLTIGGETLTARLQHLEGDAVAVTLNGHRRRLQARRDGNV 581

Query: 590 HVRTPRQAELARLMPEKLPP------DTSKMLLCPMPGLIVKVDVEVGQEVQEGQALCTI 643
            V    + E  RL   ++        +    L  PM G +V + VE GQ+V++G  L  +
Sbjct: 582 VVMVDPRGE-TRLFWRRIDAIDHGHHEAESTLTAPMHGTVVALLVEAGQKVEKGMPLMVM 640

Query: 644 EAMKMENILRAEKKGVVAKINASAGNSLAVDDVIMEF 680
           EAMKME+ + A   G V   + +AG+++   DV++EF
Sbjct: 641 EAMKMEHTMTAPADGHVESFHFNAGDTVGQGDVLLEF 677


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: 1139
Number of extensions: 64
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: 681
Length adjustment: 39
Effective length of query: 642
Effective length of database: 642
Effective search space:   412164
Effective search space used:   412164
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 24 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
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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
the source code
instructions for running GapMind on your computer

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