GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lacZ in Caulobacter crescentus NA1000

Align β-galactosidase (GalD) (EC 3.2.1.23) (characterized)
to candidate CCNA_02891 CCNA_02891 beta-galactosidase

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



>lcl|FitnessBrowser__Caulo:CCNA_02891 CCNA_02891 beta-galactosidase
          Length = 628

 Score =  316 bits (810), Expect = 2e-90
 Identities = 206/567 (36%), Positives = 285/567 (50%), Gaps = 47/567 (8%)

Query: 22  PLLLSSLAVALAACQSGEPDSAAKPQAAATPGTTAPATAPAAAPATQTPMPQFVSKDGKH 81
           PL +S+         + EP S+       TP   A     AA  A   P P+    DG  
Sbjct: 75  PLTISARPATFDIDLTSEPRSSDLTMHRLTPALAALLLGLAATSAHAEPAPRIAKIDGVQ 134

Query: 82  ALMVDGAPFLILGAQVNNSSNYP-GVMDKVWPAMQVLGPNTVQVPIAWEQVEPEEGKFDF 140
            L+V+  P+LILG ++ NSS+     +   W  M+    NTV  P+AWEQVEP EGKFDF
Sbjct: 135 RLLVNDKPYLILGGELGNSSSSDLKDLSGHWAVMKAANLNTVLAPVAWEQVEPVEGKFDF 194

Query: 141 SFVDTLLAQAREHKVRLVLLWFATWKNNGPAYAPHWVKTDNQRFPRVVTREGKAIGSLSP 200
           + +D ++ QAR H++RLVLLWF  WKN+   Y P WVK D  RFP   T EGKA+  LS 
Sbjct: 195 TVLDGMIQQARAHEMRLVLLWFGAWKNSMSTYTPAWVKRDPARFPYARTGEGKAVEILSA 254

Query: 201 HAQATLDADRKAFVAFMQHLKQVD-PQHTVIMIQPENEPGTYGSVRDFSPMAQKLFDGPV 259
              AT DAD KAF A M HLK VD  + TV+M+Q ENE G     RD +  A+  F+ PV
Sbjct: 255 SYPATRDADAKAFAAMMAHLKAVDGDKRTVLMVQVENEIGMLPEARDRTKAAEADFNKPV 314

Query: 260 PDELLKRLN-----KQPGSWAQVFGAD--ADEIFHAWSIGRYIDQVAEAGKQAYPLPMYV 312
           P   LK L+     K+ G+W +VFGA    DE++ AW+ GRY++ +A AGK+AY LPM+V
Sbjct: 315 PAAALKVLSGQIKGKKAGTWEEVFGASLATDELWQAWTFGRYVEALAAAGKKAYDLPMFV 374

Query: 313 NAALRGPFNPGQPGQYASGGPTDNVLDVWKAAGPHIDLLAPDIYMPEYRMYTTVLERYAR 372
           NAAL  P     PG Y S GP  +++D+W+AA P +D+L+PDIY P    +T  +  Y R
Sbjct: 375 NAALPRP--GAVPGGYPSAGPLPHLIDLWRAAAPSLDMLSPDIYYPN---FTEWMPPYDR 429

Query: 373 PDNALFVAE---TGNRPEYARYLFPTLGHDGVGWSAFGMDYTRYSNYPLGAKHVNEETLA 429
           PD  LF+ E    G  P      +    HD +G+S F ++            H+  E + 
Sbjct: 430 PDQPLFIPEADQAGKTPAPGNAFWAIGEHDAIGFSPFSIE------------HLPPEGVK 477

Query: 430 PFALGFKLVSLGMRPFAKAASEGKLHGTAEEPGQAVQELKLNDR------WSATITYGVP 483
                ++L+   + P       GK       P      + L  R      W  T+T   P
Sbjct: 478 TLGAAYRLLD-QLTPLITTHDGGKTMRGFRAPVAYDGTVDLTPRKASFGPWDFTVTVVDP 536

Query: 484 QFWFKGEPPGNPEPIGA--ALIAELGPDEFLVTGYHVRVTLHPASEATANMLYDRVEEGQ 541
             W     P + +   A   L+ + G DEF+V G  + +T    +    ++  + V E +
Sbjct: 537 --W----TPKDKQDYAAHGGLVIQTGADEFIVAGRGITMTF---ATKDGSVGLETVRELR 587

Query: 542 YDGDTWQFQRNWNGDQTDYGVNFSSAP 568
           ++   W   R  NGDQT  G +    P
Sbjct: 588 FENGQWVDGRWLNGDQTHQGRHIRLPP 614


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: 1099
Number of extensions: 59
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: 579
Length of database: 628
Length adjustment: 37
Effective length of query: 542
Effective length of database: 591
Effective search space:   320322
Effective search space used:   320322
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 Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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:

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:

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:

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