Alignments for a candidate for lacZ in Pedobacter sp. GW460-11-11-14-LB5

GapMind for catabolism of small carbon sources

Alignments for a candidate for lacZ in Pedobacter sp. GW460-11-11-14-LB5

Align β-galactosidase (Gal35I;GalC) (EC 3.2.1.23) (characterized)
to candidate CA265_RS02480 CA265_RS02480 beta-galactosidase

Query= CAZy::AAP86763.1
         (613 letters)



>FitnessBrowser__Pedo557:CA265_RS02480
          Length = 620

 Score =  498 bits (1281), Expect = e-145
 Identities = 268/607 (44%), Positives = 363/607 (59%), Gaps = 15/607 (2%)

Query: 2   LRTTLAPLVLALAIALPITATAASDDQWPTFATQGTQFVRDGKPYQVLSGAIHFQRIPRA 61
           L  T+  ++LAL   +P+ A      +  TFA     F+ DGKP+Q++SG IH+ RIPR 
Sbjct: 3   LFNTIRAVILALLFTIPVFA-----QETHTFALGDDAFLLDGKPFQMISGEIHYPRIPRE 57

Query: 62  YWKDRLQKARALGLNTVETYVFWNLVEPQQGQFDFNANNDVAAFVREAAAQGLNVILRPG 121
            W+ R++ A+A+GLNT+ TYVFWNL EPQ+G FDF  NNDVA FVR A  +GL VILRP 
Sbjct: 58  AWRSRMKMAKAMGLNTIGTYVFWNLHEPQKGIFDFKGNNDVAEFVRIAKEEGLWVILRPS 117

Query: 122 PYACAEWETGGYPAWLFGKDNIRVRSRDPRFLAASQAYLDAVSKQVHPLLNHNGGPIIAV 181
           PY CAEWE GGYP WL  +  + VRS+DP +L   + Y+  V KQ+ PL  ++GG I+ V
Sbjct: 118 PYVCAEWEFGGYPYWLENEKGLVVRSKDPLYLKEYEKYIMEVGKQLAPLQVNHGGNILMV 177

Query: 182 QVENEYGSYDDDHAYMADNRAMYVKAGFDDALLFTSDGADMLANGTLPDTLAVVNFAPGE 241
           Q+ENEYGSY  D  Y++ N+ +++KAGF D LL+T D A  L NG LP  L  VN     
Sbjct: 178 QIENEYGSYGSDKEYLSINQKLFIKAGF-DGLLYTCDPAPDLTNGYLPGLLPAVNGLDNP 236

Query: 242 AKSAFDKLI--KFRPDQPRMVGEYWAGWFDHWGKPHASTDAKQQTEELEWILRQGHSANL 299
            K    KLI        P  + E++  WFD WG PH +  A + T +L+ +L  G S N+
Sbjct: 237 EK--VKKLIADHHNGKGPYYIAEWYPAWFDWWGAPHHTVPAARFTGKLDSVLAAGISINM 294

Query: 300 YMFIGGTSFGFMNGANFQGNPSDHYAPQTTSYDYDAILDEAGRATPKFALMRDAITR--V 357
           YMF GGT+ GFMNGANF+      Y PQ +SYDYDA LDEAG AT KF   R  I +   
Sbjct: 295 YMFHGGTTRGFMNGANFKDETP--YEPQISSYDYDAPLDEAGNATAKFHAFRSIIQKHLP 352

Query: 358 TGVQPPALPAPIAIAALPETQLRESTSLWDNLPAPIAIDTPQPMEHFGQDYGYILYRTTV 417
            G   P +P P     +P  +L  + SL  NL      D+P   E   QDYG++LYRTT+
Sbjct: 353 AGTTLPPVPNPKPAIRIPTIKLGLTASLTGNLSKGTYHDSPLTFEELLQDYGFVLYRTTL 412

Query: 418 TGPRKGALYLGEVRDVARVYLDKKPVGSVERRLQQVSTNVDIPAGEHTLDVLVENSGRIN 477
           TG  KG L + E+RD A + ++ K + +++RRL Q S N+ +P G+  LD+LVEN GRIN
Sbjct: 413 TGGIKGTLKIKELRDYALIMVNGKQIATLDRRLNQDSLNISLPQGKVVLDILVENLGRIN 472

Query: 478 YGPRMADGRAGLVDPVLLDNRQLTGWQAFPLPMRSPDSLR-GWTRNHVDGPAFHRGTLRI 536
           +G  +   R G+   V  +NR++ GW  +  P      ++   T    + P   +GT  +
Sbjct: 473 FGKYLLQNRKGITGYVSFNNRKIKGWTMYRFPFNDLSKIKYQSTVKAGNTPVIKKGTFNL 532

Query: 537 DTPTDTYLDMRAFGKGVTWTNGVNLGRHWNIGAQRALYFPAPFQRKGDNTVVVFDLDSTA 596
               DTYLDMR +GKG+ W NG NLG++W+IG Q  LY PA + RKG N++ V +L    
Sbjct: 533 TAIGDTYLDMRKWGKGMVWVNGHNLGKYWSIGPQETLYLPAEWLRKGVNSIEVLELLRPN 592

Query: 597 KPSVRGL 603
           +  + G+
Sbjct: 593 QNEITGI 599


Lambda     K      H
   0.320    0.136    0.427 

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: 1144
Number of extensions: 55
Number of successful extensions: 7
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: 613
Length of database: 620
Length adjustment: 37
Effective length of query: 576
Effective length of database: 583
Effective search space:   335808
Effective search space used:   335808
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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