Alignments for a candidate for lacZ in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for lacZ in Caulobacter crescentus NA1000

Align β-galactosidase (GalD) (EC 3.2.1.23) (characterized)
to candidate CCNA_00830 CCNA_00830 beta-galactosidase

Query= CAZy::ABA39423.1
         (579 letters)



>FitnessBrowser__Caulo:CCNA_00830
          Length = 549

 Score =  634 bits (1636), Expect = 0.0
 Identities = 310/524 (59%), Positives = 378/524 (72%), Gaps = 8/524 (1%)

Query: 62  AAAPATQTPMPQFVSKDGKHALMVDGAPFLILGAQVNNSSNYPGVMDKVWPAMQVLGPNT 121
           + A A    MPQ V+KDG+HALMVDGAPFL+L AQVNNSS +P  M KVWPA++ +G NT
Sbjct: 27  SGAHAADAAMPQLVTKDGRHALMVDGAPFLMLAAQVNNSSAWPSQMAKVWPAIEKVGANT 86

Query: 122 VQVPIAWEQVEPEEGKFDFSFVDTLLAQAREHKVRLVLLWFATWKNNGPAYAPHWVKTDN 181
           VQVPIAWEQ+EP EG+FDFS++D LL QARE KVRLVLLWF TWKN+ P+YAP WVK D+
Sbjct: 87  VQVPIAWEQIEPVEGQFDFSYLDLLLEQARERKVRLVLLWFGTWKNSSPSYAPEWVKLDD 146

Query: 182 QRFPRVVTREGKAIGSLSPHAQATLDADRKAFVAFMQHLKQVDP-QHTVIMIQPENEPGT 240
           +RFPR++  +G+   S+SP A++TLDADRKAFVA M HLK  D  Q TVIM+Q ENE GT
Sbjct: 147 KRFPRLIKDDGERSYSMSPLAKSTLDADRKAFVALMTHLKAKDAAQKTVIMVQVENETGT 206

Query: 241 YGSVRDFSPMAQKLFDGPVPDELLKRLNKQPGSWAQVFGADADEIFHAWSIGRYIDQVAE 300
           YGSVRDF P AQK+F+GP P  L+K +  +PG+W+Q FG DADE FHAW IGR++DQVA 
Sbjct: 207 YGSVRDFGPAAQKVFNGPAPATLVKAVGAKPGTWSQAFGKDADEFFHAWHIGRFVDQVAA 266

Query: 301 AGKQAYPLPMYVNAALRGPFNPGQPGQYASGGPTDNVLDVWKAAGPHIDLLAPDIYMPEY 360
            GK  YPLPMYVNAALR P  PG P  Y++GGPTDNV+ VW+AA P IDL+APDIYM E 
Sbjct: 267 GGKAVYPLPMYVNAALRDPIKPGDPKTYSAGGPTDNVIGVWQAAAPSIDLIAPDIYMKES 326

Query: 361 RMYTTVLERYARPDNALFVAETGNRPEYARYLFPTLGHDGVGWSAFGMDYTRYSNYPLGA 420
             Y  VL  YARP+NALFVAETGN P YARY+F TLG  G+GWS FGMDYT Y NYPLGA
Sbjct: 327 VKYEAVLGHYARPNNALFVAETGNDPAYARYVFSTLGKQGIGWSPFGMDYTGYGNYPLGA 386

Query: 421 KHVNEETLAPFALGFKLVSLGMRPFAKAASEGKLHGTAEEPGQAVQELKLNDRWSATITY 480
             V+E  +  FA  ++L++   R  A+ + EGK+ G AE   +A Q   + D W+ ++ Y
Sbjct: 387 AKVDEALIEVFAANYRLLAPMARELARLSFEGKVWGGAEPDDRAAQTTTMGD-WTVSLRY 445

Query: 481 GVPQF------WFKGEPPGNPEPIGAALIAELGPDEFLVTGYHVRVTLHPASEATANMLY 534
           G  QF      W K  PPG   P G  L+A+L P+EFLVTG +VRV    A+     M+ 
Sbjct: 446 GKWQFGASDWTWLKDRPPGPQGPEGGGLVAQLSPNEFLVTGRNVRVEFGRATADGKPMMM 505

Query: 535 DRVEEGQYDGDTWQFQRNWNGDQTDYGVNFSSAPQLLKIKLATY 578
            RVEEG ++   W F R WNGDQTDYG+NF+   Q+L++KLATY
Sbjct: 506 ARVEEGHFENGQWVFDRLWNGDQTDYGLNFTGGSQILRVKLATY 549


Lambda     K      H
   0.317    0.134    0.419 

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: 1091
Number of extensions: 42
Number of successful extensions: 4
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: 579
Length of database: 549
Length adjustment: 36
Effective length of query: 543
Effective length of database: 513
Effective search space:   278559
Effective search space used:   278559
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: 53 (25.0 bits)

This GapMind analysis is from Apr 09 2024. 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 2024 update 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