Alignments for a candidate for bgl in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for bgl in Caulobacter crescentus NA1000

Align Beta-glucosidase (EC 3.2.1.21) (characterized)
to candidate CCNA_02131 CCNA_02131 glucan 1,4-beta-glucosidase

Query= reanno::Korea:Ga0059261_1166
         (834 letters)



>FitnessBrowser__Caulo:CCNA_02131
          Length = 821

 Score =  831 bits (2146), Expect = 0.0
 Identities = 431/808 (53%), Positives = 538/808 (66%), Gaps = 40/808 (4%)

Query: 37  AQAHPAMWP-ERRPTVPLDPAVELRVADLLAKMSLEQKVGQIIQADIASVTPADVHRYHL 95
           A A+PA+WP    P    D   E  +A L+++M++E+KV Q IQAD AS+TP ++ +Y L
Sbjct: 32  ATANPAVWPMSASPAAITDAKTEAFIAQLMSRMTVEEKVAQTIQADGASITPEELKKYRL 91

Query: 96  GSVLNGGNSDPGGRYNAPPRDWLAAADAFYAASMQPNGALPRIPVIWGSDAVHGHNNVVG 155
           GSVL GGNS P G   A P+ W+    AF AA++   G    IP+I+G DAVHGHNNVVG
Sbjct: 92  GSVLVGGNSAPDGNDRASPQRWIEWIRAFRAAALDKRGDRQEIPIIFGVDAVHGHNNVVG 151

Query: 156 ATLFPHNIGLGAARNPDLIRRIGEATAIEMRVTGLDWTFAPTLAVVRDDRWGRTYEGFGE 215
           AT+FPHN+GLGAA  PDLIRRIGE TA EM  TG DWTF PT+AV RD RWGR YEG+GE
Sbjct: 152 ATIFPHNVGLGAAHEPDLIRRIGEVTAKEMAATGADWTFGPTVAVPRDSRWGRAYEGYGE 211

Query: 216 TPEIATAYAAPLIEGLQGKIGDKDWLRGPHIIATAKHFLGDGGTRNGKDQGDTEIGEAGL 275
            PEI  AY+ P+  GLQG +     L    +  +AKHFL DGGT NG+DQGD +I EA L
Sbjct: 212 NPEIVKAYSGPMTLGLQGALEAGKPLAAGRVAGSAKHFLADGGTENGRDQGDAKISEADL 271

Query: 276 RDLFSPPYLPALDAGVQSVMVSFSGWNGAKMHGNKSLLTGVVKQRWNFDGFLVGDWNGHG 335
             L +  Y PA++AG+ SVMVSFS WNG K  GNKSLLT V+K+R  F+GF+VGDWN HG
Sbjct: 272 VRLHNAGYPPAIEAGILSVMVSFSSWNGVKHTGNKSLLTDVLKERMGFEGFVVGDWNAHG 331

Query: 336 QVAGCTATNCPQSAIAGLDMYMAPDSWKALYEATLGQARDGTLPIDRLDDAVRRILRVKI 395
           QV GC+ T+C Q+  AG+DM MAPDSWK LY+ TL Q + G +P+ R+DDAVRRILRVK+
Sbjct: 332 QVEGCSNTSCAQAYNAGMDMMMAPDSWKGLYDNTLAQVKAGQIPMARIDDAVRRILRVKV 391

Query: 396 RAGLFEAGKPSSRPYAGRYELLGSAEHRALAREAVRQSLVLLKNANGLLPLKPGGRILVA 455
           +AGLFE      RP  G+ ELLG+ EHRA+AREAVR+SLVLLKN  G+LPLK   R+LVA
Sbjct: 392 KAGLFE----DKRPLEGKLELLGAPEHRAVAREAVRKSLVLLKN-EGVLPLKSSARVLVA 446

Query: 456 GDGADNLTKQTGGWTLSWQGTGTQRSDFPNAQSIWEGIEATVKAAGGTATLSVEGGYSAK 515
           GDGAD++ K +GGWTL+WQGTG + SDFP+ QSI+ G+   VKA GG+A LSV G +  K
Sbjct: 447 GDGADDIGKASGGWTLTWQGTGNKNSDFPHGQSIYAGVAEAVKAGGGSAELSVSGDFKQK 506

Query: 516 PDAAIVVFGEEPYAEFQGDRPDVGYD--DAKTLALLRTLKTAGVPTVAVFLSGRAMWVNP 573
           PD AIVVFGE PYAEFQGD   + Y   D + LALL+ LK AG+P V+VFLSGR +W NP
Sbjct: 507 PDVAIVVFGENPYAEFQGDITSIEYQAGDKRDLALLKKLKAAGIPVVSVFLSGRPLWTNP 566

Query: 574 FLNASDAFVAAWLPGSEGGGVADVLFG------KSDFSGKLGYSWPRSSDQTTVNIGDSN 627
            LNASDAFVAAWLPGSEGGGVADVL G      + DF GKL +SWP+ +DQ  +N+GD  
Sbjct: 567 ELNASDAFVAAWLPGSEGGGVADVLVGDKAGKPRHDFQGKLSFSWPKRADQEPINVGDPG 626

Query: 628 YDPLFPYGFGLKVADRGDLAALPETRATA-AAAETGILFTAGKPGGGRRLLLGRPGELAA 686
           YDPLF YG+GL  A  G +A L E    A AAA     F  G+                 
Sbjct: 627 YDPLFAYGYGLSYAKPGKVAKLSEDPGVASAAANVDRYFVDGR----------------- 669

Query: 687 NPGPELIDA------RPADRSAQEDSLRIRWTGAGQAVAAIVQDVPVDLSRQANGDLALE 740
            P P +++A      +  D  AQE++ +  W+G G  V  ++   PVDLSRQ  GD+A+ 
Sbjct: 670 TPPPWMMNASGAASLKTVDAGAQENARQATWSGEGLGVVGVMGS-PVDLSRQTTGDMAVM 728

Query: 741 LELKVNAAPSAEVSLLMRCGTDCAGGFPVRGILGEAAKTGKWTRVAVPLRCFEKAGVDMT 800
           L  +V AAP+  VS+ + CG  C     V   L   AKTG+W    + L CF   G DMT
Sbjct: 729 LRYRVEAAPTKPVSMSVTCGESCRATVDVTSTL-SGAKTGEWRTAKIKLSCFLAKGADMT 787

Query: 801 RVETPLSIATAGSLDLTLSSARITSPSG 828
           ++ +P ++ TAG+L L+ +  R+ S  G
Sbjct: 788 QISSPFALTTAGALTLSFTEIRLASNEG 815


Lambda     K      H
   0.317    0.135    0.412 

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: 2064
Number of extensions: 110
Number of successful extensions: 8
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: 834
Length of database: 821
Length adjustment: 42
Effective length of query: 792
Effective length of database: 779
Effective search space:   616968
Effective search space used:   616968
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 (21.6 bits)
S2: 56 (26.2 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