Alignments for a candidate for lacZ in Jannaschia aquimarina GSW-M26

GapMind for catabolism of small carbon sources

Alignments for a candidate for lacZ in Jannaschia aquimarina GSW-M26

Align β-galactosidase (EC 3.2.1.23) (characterized)
to candidate WP_043920531.1 jaqu_RS18705 beta-galactosidase

Query= CAZy::ABI35985.1
         (645 letters)



>NCBI__GCF_000877395.1:WP_043920531.1
          Length = 642

 Score =  622 bits (1605), Expect = 0.0
 Identities = 328/629 (52%), Positives = 400/629 (63%), Gaps = 26/629 (4%)

Query: 2   LGVCYYPEHWPKERWKEDARRMREAGLSHVRIGEFAWALLEPEPGRLEWGWLDEAIATLA 61
           LGVCYYPEHWP++RW  DA  M EAGL+ VRIGEFAW+ LEP PG L + WL  AI TL 
Sbjct: 5   LGVCYYPEHWPEDRWATDATMMAEAGLTWVRIGEFAWSRLEPAPGELRFDWLARAIDTLR 64

Query: 62  AEGLKVVLGTPTATPPKWLVDRYPEILPVDREGRRRRFGGRRHYCFSSPVYREEARRIVT 121
             GLK+VLGTP+ATPP W++DR+P++L VD EGR R+FG RRHYCFS   YR+EA R+  
Sbjct: 65  GAGLKIVLGTPSATPPHWMLDRHPDMLAVDAEGRPRKFGSRRHYCFSHVPYRDEAARMAR 124

Query: 122 LLAERYGGLEAVTGFQTDNEYGCHDTVRCYCPRCQEAFRGWLEARYGT------IEALNE 175
           LLAER+  ++A   +QTDNEYGCHDT+  +    ++AFR WL  RY        I ALN 
Sbjct: 125 LLAERFPDVDA---WQTDNEYGCHDTILSWSDAARDAFRDWLRERYSKAGANDPIGALNA 181

Query: 176 AWGTAFWSQRYRSFAEVELPHLTVAEPNPSHLLDYYRFASDQVRAFNRLQVEILRAHAPG 235
            WG  FWS  Y  F +++LP+LTV EPNP+HL+ + RF+SDQV  +N  QVE +R H+  
Sbjct: 182 HWGNVFWSMDYADFDQIDLPNLTVTEPNPAHLMAFRRFSSDQVARWNAAQVEAIRVHSDA 241

Query: 236 KFVTHNFMGFFTDLDAFALAQDLDFASWDSYPLGFTDLMPLPPEEKLRYARTGHPDVAAF 295
             ++HN+MG  T+ D + L + ++ A+WDSYPLGF  L  +P  +   Y R G PD  AF
Sbjct: 242 P-ISHNYMGRITEFDHYDLGRQMEIATWDSYPLGFL-LDRVPDGDAQAYLRQGDPDFQAF 299

Query: 296 HHDLYRGVGRG-------RFWVMEQQPGPVNWAPHNPSPAPGMVRLWTWEALAHGAEVVS 348
           HHDLYR V          R+WVMEQQPGPVNWAPHNP+P PGMVRLWTWEA AHGAE V 
Sbjct: 300 HHDLYRAVAAQAPGDAPPRWWVMEQQPGPVNWAPHNPAPLPGMVRLWTWEAFAHGAEAVC 359

Query: 349 YFRWRQAPFAQEQMHAGLHRPDSAPDQGFFEAKRVAEELAALALPPVAQAPVALVFDYEA 408
           YFRWRQAPFAQE  HAGL RPD+ P  G  EA+ VA ELA       AQAPVALVFDY +
Sbjct: 360 YFRWRQAPFAQESHHAGLLRPDAEPAPGLAEARAVAAELADAPDVASAQAPVALVFDYAS 419

Query: 409 AWIYEVQPQGAEWSYLGLVYLFYSALRRLGLDVDVVPPGA-SLRGYAFAVVPSLPIVREE 467
            W +EVQPQG  + +  L +  Y ALR LGL VD++PP A SL GYA  ++PSL  +   
Sbjct: 420 QWAWEVQPQGKGFDHFALAFHLYRALRSLGLGVDILPPDAPSLDGYALTLIPSLMTLGSA 479

Query: 468 ALEAFREAEGPVLFGPRSGSKTETFQIPKELPPGPLQALLPLKVVRVESLPPGLLEVAEG 527
              A  EA G VL GPR+  +     +   +P GP    L +    VE+LPP     A  
Sbjct: 480 LRGAIEEAPGIVLTGPRTDLRGP--DLAMHVPLGPHLPGLDVTATLVETLPPH----APR 533

Query: 528 ALGR-FPLGLWREWVEAPLKPLLTFQDGKGALYREGRYLYLAAWPSPELAGRLLSALAAE 586
           AL R   L LW E +E     +    DG  AL R G   +LA WP  E A R+L  LA E
Sbjct: 534 ALRRGGALTLWLEHLETDAAIVEHTTDGLPALVRSGNRAHLAGWPDMEAARRILRDLATE 593

Query: 587 AGLKVLSLPEGLRLRRRGTWVFAFNYGPE 615
           AGL  + +PEG+R R   T  F FNY  E
Sbjct: 594 AGLDPIDMPEGVRRRGTATETFLFNYAAE 622


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: 1550
Number of extensions: 86
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: 642
Length adjustment: 38
Effective length of query: 607
Effective length of database: 604
Effective search space:   366628
Effective search space used:   366628
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 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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