Alignments for a candidate for pccA in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for pccA in Cupriavidus basilensis 4G11

Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate RR42_RS32735 RR42_RS32735 3-methylcrotonyl-CoA carboxylase

Query= reanno::Dino:3607308
         (681 letters)



>FitnessBrowser__Cup4G11:RR42_RS32735
          Length = 674

 Score =  454 bits (1169), Expect = e-132
 Identities = 276/691 (39%), Positives = 392/691 (56%), Gaps = 40/691 (5%)

Query: 2   FKKILIANRGEIACRVIKTARKMGIQTVAIYSDADRNALHVRMADEAVHIGPSPANQSYI 61
           F  +L+ANRGEIA R+++TAR++G+ TVA+YS+ADR+  HV  AD AV IG +    SY+
Sbjct: 8   FHTLLVANRGEIAMRIMRTARRLGLATVAVYSEADRHGPHVAYADRAVRIGDAAPRASYL 67

Query: 62  VIDKVMDAIRQTGAEAVHPGYGFLSENKLFAEALEKEGVAFIGPPANAIEAMGDKITSKK 121
            I  +++A R++GA+AVHPGYGFL+EN  FA+A+ + G+ F+GPPA AI AMG+K  +K+
Sbjct: 68  NIAAIIEAARRSGADAVHPGYGFLAENAEFADAVAQAGLVFVGPPAAAIRAMGNKAEAKR 127

Query: 122 IAQEANVSTVPGYMGLIADADEAVKISGEIGYPVMIKASAGGGGKGMRIAWNDAEAREG- 180
           +   A++  +PGY G   D    ++ +  IG+P+M+KA+AGGGG+GMR+  +D  A  G 
Sbjct: 128 LMLAADMPCIPGYQGEAQDDAALLQAAAPIGFPLMVKAAAGGGGRGMRLV-HDVHALPGA 186

Query: 181 FQSSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADTHGNCIYLGERECSIQRRNQKVVE 240
             S+++EA  +FG  ++ +E+ V  PRH+EIQV ADT G+ I+LGER+CS+QRR+QKVVE
Sbjct: 187 LASARSEAMAAFGSGQLILERAVIAPRHVEIQVFADTQGHVIHLGERDCSVQRRHQKVVE 246

Query: 241 EAPSPFLDEATRKAMGEQSCALAQAVGYASAGTVEFIVDGDRNFYFLEMNTRLQVEHPVT 300
           EAPSP +  A R+ MG  +   AQA+GY  AGT+EF++DGD NFYF+EMNTRLQVEH VT
Sbjct: 247 EAPSPAVSPALRERMGGAAVRAAQAIGYVGAGTMEFLLDGDGNFYFMEMNTRLQVEHAVT 306

Query: 301 ELITGVDLVEQMIRVAAGEKLPMTQDDVTLTGWAIENRLYAEDPYRNFLPSIGRLTRYRP 360
           E ITG DLVE  +RVAAGE LP+TQ+ V L G AIE RL AED    FLP  G + R+R 
Sbjct: 307 EAITGFDLVEWQLRVAAGEPLPVTQEQVALRGHAIEVRLTAEDVAAGFLPQGGPVLRWR- 365

Query: 361 PVEVAAGPLEANGKWHGDAPSGPTAVRNDTGVYEGGEISMYYDPMIAKLCTWGPDRPAAI 420
                             AP     VR D  + EGGEI ++YD M+AKL T G  R  A 
Sbjct: 366 ------------------APGAGHDVRVDHALQEGGEIPVHYDSMVAKLVTHGATREEAR 407

Query: 421 EAMRNALDGFEVEGIGHNLPFVAAVMDHPVFIKGEMTTAFIKEQYPDGFEGVTLGAADLT 480
             +  A++   + G+  N  F+A  + H  F   ++ T F+              AA + 
Sbjct: 408 RKLLRAVEQTVLLGVASNQGFLADCLAHEAFAGNQVHTGFVDTHMQAALRTTQPAAAQVA 467

Query: 481 RLAAAAAAMFRVAE---IRRTRISGTLDNHERMVGTDWVVTAQDARFDVTIDADPG-GST 536
             A AAA +   +E   +     S  L   E+    D    AQ   ++V +    G G  
Sbjct: 468 CAALAAAGLLAASECPALVAPACSLGLQAGEQQWRVDLRAVAQG--WEVAVRGGEGEGEG 525

Query: 537 VRFADGTAHRVTS----RWTPGDSLATVEIDGAPMVLKVDKITSGFRMRFRGADVKVHVR 592
               DGT+  + S    R       A VE +G  M L +   T G  +    A      R
Sbjct: 526 EGEGDGTSAEIVSVRVLRADLEQGSALVECNG--MALPLVFATGGDAVHLFSAG-----R 578

Query: 593 TPRQAELNDLMPEKLPPDTSKM--LLCPMPGLVVKIDVEVGDEVQEGQALCTVEAMKMEN 650
             R A L+    ++ P D  +   LL P+   +V +    G+ V  GQ L  +EAMKME+
Sbjct: 579 AWRFARLDPRQKKRNPGDAGRAGELLAPLTARIVAVKAAAGEAVLAGQVLVVLEAMKMEH 638

Query: 651 ILRAEKTATVTKINAGAGDSLAVDDVIMEFE 681
            + A     + +++A  G       ++++ +
Sbjct: 639 AIVAPFDGVIAQLHAREGGQARAGSLLVKVD 669


Lambda     K      H
   0.318    0.134    0.392 

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: 1136
Number of extensions: 56
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: 674
Length adjustment: 39
Effective length of query: 642
Effective length of database: 635
Effective search space:   407670
Effective search space used:   407670
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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