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

GapMind for catabolism of small carbon sources

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

Align β-galactosidase L+M (LacL+LacM) (EC 3.2.1.23) (characterized)
to candidate CA265_RS04025 CA265_RS04025 glycoside hydrolase family 2

Query= CAZy::AAA25267.1
         (626 letters)



>FitnessBrowser__Pedo557:CA265_RS04025
          Length = 1054

 Score =  361 bits (927), Expect = e-104
 Identities = 223/643 (34%), Positives = 339/643 (52%), Gaps = 55/643 (8%)

Query: 8   LDDPEVFRVNQLPAHSDHHYYHD----TAEFKTGSRFIKSLNGAWRFNFAKTPAERPVDF 63
           L  PEV  VN+LP  +    + +    T   K  S +  SLNG W+FN+ K P +RP DF
Sbjct: 27  LQTPEVVSVNRLPMRASAFAFENQDLATKRAKEKSEYFLSLNGTWKFNWVKDPRKRPTDF 86

Query: 64  YQPDFDATDFDTIQVPGHIELAGYGQIQYINTLYPWEGKIYRRPPYTLNQDQLTPGLFSD 123
           Y+ DFD   +D  +VP + E  GYG   Y+N  Y + G+        L   ++ P     
Sbjct: 87  YKLDFDDKGWDNFKVPANWETNGYGTPIYVNQPYEFAGR-------QLTGARMNPPFDIP 139

Query: 124 AADNTVGSYLKTFDLDDVFKGQRIIIQFQGVEEALYVWLNGHFIGYSEDSFTPSEFDLTP 183
           A +N VGSY K  ++   + G+++ I    V+ A Y+W+NG  +GYSEDS   +EFD+T 
Sbjct: 140 ADNNPVGSYRKKINIPANWSGRQVFISLGAVKSAFYIWVNGKKVGYSEDSKLAAEFDITK 199

Query: 184 YIQDQGNVLAVRVYKHSTAAFIEDQDMFRFSGIFRDVNILAEPASHITDLDIRPVPNANL 243
           Y++   N +A++VY+ S   ++E QDM+R SGI R+V + + P   I D  +    +A  
Sbjct: 200 YVKPGENTIALQVYRWSDGTYLECQDMWRISGIEREVYLYSTPKLDIRDFKVIGNLDATY 259

Query: 244 KSGELNITTKVTG------------EPATLALTVKDHDGR-----VLTSQTQTGS--GSV 284
            +G LN+   V              +   +AL + D  G        T Q   G+    +
Sbjct: 260 TNGLLNVDLAVENYKIDQRTNHSRPDSFYVALDLVDAKGNNVWKDATTIQKVLGNYKTDL 319

Query: 285 TFDTMLFDQLHLWSPQTPYLYQLTIEVYDADHQLLEVVPYQFGFRTVELRDDKVIYVNNK 344
           +F T +   +  WS + PYLY L I + D +++++EV+P + GFR+VE++   ++ VN K
Sbjct: 320 SFKTQI-SNVKNWSAEIPYLYTLYITLKDKNNKIIEVIPQRVGFRSVEIKGSDLL-VNGK 377

Query: 345 RLVINGVNRHEWNAHTGRVISMADMRADIQTMLANNINADRTCHYPDQLPWYQLCDEAGI 404
           R+ + GVNRHE NA  G  ++ ADM  D++ M   N+NA R  HYP    W +LCDE G+
Sbjct: 378 RVFLKGVNRHEHNATQGHTLTHADMEKDMEMMKKLNVNAVRHSHYPPDPYWMELCDEYGL 437

Query: 405 YLMAETNLESHGSWQKMGAIEPSYNVPGDNPHWPAAVIDRARSNYEWFKNHPSIIFWSLG 464
           Y++ E N+ESHG +    ++E ++    ++  W    ++R    YE  KNH S+I WSLG
Sbjct: 438 YVIDEANIESHGRYY---SLETTF---ANDKQWRIPHLERITRMYERDKNHASVITWSLG 491

Query: 465 NESYAGEDIAAMQAFYKEHDDSRLVHYEGVFYTPELKDRISDVESRMYEKPQNIVAY-LE 523
           NE+  G +      FY+ +   +   +  V Y     D  +D+    Y  P  +  Y  +
Sbjct: 492 NEAGNGVN------FYEAYQWLKGKDFRPVQYERAESDFNTDMIVPQYPSPNYLPRYSKQ 545

Query: 524 DNPTKPFLNCEYMHDMGNSLGGMQSYNDLIDKYPMYQGGFIWDFIDQALFVHDPITD-QD 582
           D  T+PF+  EY H MGNSLG  + Y D I+  P  QGGF+W++IDQA+   D + + + 
Sbjct: 546 DKETRPFIMSEYAHIMGNSLGNFKEYWDAIENNPKLQGGFVWEWIDQAI---DTVKNGKR 602

Query: 583 VLRYGGDF------DERHSDYAFSGNGLMFADRTPKPAMQEVK 619
           ++ YGGDF      DE  SD  F   G++ A R   P   E+K
Sbjct: 603 IMAYGGDFPLSGPVDENFSDNDFCVKGVVTAYRGMTPMAVELK 645


Lambda     K      H
   0.320    0.138    0.430 

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: 1910
Number of extensions: 108
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: 626
Length of database: 1054
Length adjustment: 41
Effective length of query: 585
Effective length of database: 1013
Effective search space:   592605
Effective search space used:   592605
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: 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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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