Alignments for a candidate for lacZ in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for lacZ in Phaeobacter inhibens BS107

Align β-galactosidase (A4-β-Gal) (EC 3.2.1.23) (characterized)
to candidate GFF718 PGA1_c07330 beta-galactosidase 1

Query= CAZy::BAA28362.1
         (645 letters)



>FitnessBrowser__Phaeo:GFF718
          Length = 639

 Score =  654 bits (1686), Expect = 0.0
 Identities = 333/623 (53%), Positives = 414/623 (66%), Gaps = 13/623 (2%)

Query: 2   LGVCYYPEHWPKERWKEDARRMREAGLSHVRIGEFAWALLEPEPGRLEWGWLDEAIATLA 61
           LG CYYPEHWP++ W+EDA RM  AGL+ VRIGEF+W+ +EP PG L+W WLD AI TL 
Sbjct: 5   LGTCYYPEHWPEDIWQEDAARMVAAGLTWVRIGEFSWSRIEPNPGDLQWDWLDRAIDTLV 64

Query: 62  AEGLKVVLGTPTATPPKWLVDRYPEILPVDREGRRRRFGGRRHYCFSSPVYREEARRIVT 121
           A GLKVVLGTPTATPP+W+VDR+P++  +D +GR R FG RRHYCFS   YR EARRIVT
Sbjct: 65  AAGLKVVLGTPTATPPRWMVDRHPDMFALDADGRSRGFGSRRHYCFSHTGYRAEARRIVT 124

Query: 122 LLAERYGGLEAVAGFQTDNEYGCHDTVRCYCPRCQEAFRGWLEARY-GTIEALNEAWGTA 180
           L+AERYG  + +A +QTDNEYGCHDT   Y P    AF  WLE R+ G I ALN AWG  
Sbjct: 125 LMAERYGPGDRIAAWQTDNEYGCHDTTISYSPAAAAAFTHWLEVRFNGDICALNAAWGNV 184

Query: 181 FWSQRYRSFAEVELPHLTVAEPNPSHLLDYYRFASDQVRAFNRLQVEILRAHAPGKFVTH 240
           FWS  Y  F ++ LP+LTV EPNP+H+  + RF+SDQV +FNR QVEILRAH+    + H
Sbjct: 185 FWSMEYERFDQIGLPNLTVTEPNPAHVQAFRRFSSDQVVSFNRDQVEILRAHSDAP-IAH 243

Query: 241 NFMGFFTDLDAFALAQDLDFASWDSYPLGFT-DLMPLPPEEKLRYARTGHPDVAAFHHDL 299
           N+MG  TD D + + +DL+ ASWDSYPLGF  D +    E++ RYAR G PD  AFHHDL
Sbjct: 244 NYMGRVTDFDHYKVGEDLEIASWDSYPLGFLEDRVGASAEDQRRYARQGDPDFQAFHHDL 303

Query: 300 YRGVGRGRFWVMEQQPGPVNWAPHNPSPAPGMVRLWTWEALAHGAEVVSYFRWRQAPFAQ 359
           YR VGRGR+WVMEQQPGPVNWAP+NP+P PGMVR WTWEA AHGAE V YFRWRQAPFAQ
Sbjct: 304 YRAVGRGRWWVMEQQPGPVNWAPYNPAPLPGMVRFWTWEAFAHGAEAVCYFRWRQAPFAQ 363

Query: 360 EQMHAGLHRPDSAPDQGFFEAKRVAEELAALALPPVAQAPVALVFDYEAAWIYEVQPQGA 419
           EQ+HAGL RPDSA      EA++VAEEL +      +QAPVAL+FDY+A W ++VQP G 
Sbjct: 364 EQLHAGLLRPDSAETPAMIEARQVAEELTSADEVAPSQAPVALLFDYDAEWAWQVQPHGK 423

Query: 420 EWSYLGLVYLFYSALRRLGLDVDVVPP-GASLRGYAFAVVPSLPIVREEALEAFREAEGP 478
             SY  LV   Y ALRR GL +D+VPP      GY   + P L  + ++   A  +A G 
Sbjct: 424 GLSYFDLVLDHYRALRRAGLSIDIVPPTQTDFTGYELILAPGLVHLPDDLRGALADATGL 483

Query: 479 VLFGPRSGSKTETFQIPKELPPGPLQALLPLKVVRVESLPPGL---LEVAEGALGRFPLG 535
            L+GPR+ ++ E F+IP    P  LQ  L + V  VESL P +   L   +GA+    +G
Sbjct: 484 RLYGPRTAARDEDFRIPTSPLPPALQG-LDIVVAAVESLRPDMPLPLANGDGAV----VG 538

Query: 536 LWREWVEAPLKPLLTFQDGKGALYREGRYLYLAAWPSPELAGRLLSALAAEAGLKVLSLP 595
            + E ++     L+    G          +Y A W  P     L++ L A AG+ +  +P
Sbjct: 539 -YLETLDGEGSVLIETSAGHAVAVAADNQVYCAGWLDPLGLDHLIATLCARAGVNIRKMP 597

Query: 596 EGLRLRRRGTWVFAFNYGPEAVE 618
           EG+R+R+  T  F FN+  E VE
Sbjct: 598 EGVRMRQTATEEFWFNHLAEPVE 620


Lambda     K      H
   0.322    0.139    0.454 

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: 1416
Number of extensions: 62
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: 645
Length of database: 639
Length adjustment: 38
Effective length of query: 607
Effective length of database: 601
Effective search space:   364807
Effective search space used:   364807
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 (21.9 bits)
S2: 54 (25.4 bits)

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

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Protein sequences (fasta format)
Organisms (tab-delimited)
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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