Alignments for a candidate for lacZ in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for lacZ in Shewanella loihica PV-4

Align β-galactosidase Z (LacZ;TmLac;TM1193) (EC 3.2.1.23) (characterized)
to candidate 5210843 Shew_3269 Beta-galactosidase (RefSeq)

Query= CAZy::AAD36268.1
         (1087 letters)



>FitnessBrowser__PV4:5210843
          Length = 1076

 Score =  727 bits (1877), Expect = 0.0
 Identities = 411/1039 (39%), Positives = 586/1039 (56%), Gaps = 75/1039 (7%)

Query: 8    WENPQLVSEGTEKSHASFIPY-LDPFS--GEWEYPEEFISLNGNWRFLFAKNPFEVPEDF 64
            W++  L        HASF  Y  +P +   E +  + ++ LNG WRF  AKNP   P++F
Sbjct: 35   WQDHTLFEVNKLAPHASFFGYESEPLALLDEMDRSQLYLDLNGRWRFHLAKNPDATPKEF 94

Query: 65   FSEKFDDSNWDEIEVPSNWEMKGYGKPIYTNVVYPFEPNPPFVPKDDNPTGVYRRWIEIP 124
             + +FD S+W  I+VP N+E +GYG  IY +  YPF+   P  P D NPTG+YR+   +P
Sbjct: 95   AAPEFDASHWGSIQVPGNFETQGYGHAIYLDERYPFDTKWPDAPSDHNPTGLYRKTFTLP 154

Query: 125  EDWFKKEIFLHFEGVRSFFYLWVNGKKIGFSKDSCTPAEFRLTDVLRPGKNLITVEVLKW 184
              W +K++F+H    RS   L+VNG+++G+S+ + TPAEF +T  L+ G NL+ +++++W
Sbjct: 155  AHWQQKQVFIHIGAARSALTLFVNGREVGYSQGAKTPAEFDITPYLQAGDNLVAMQLIRW 214

Query: 185  SDGSYLEDQDMWWFAGIYRDVYLYALPKFHIRDVFVRTDLDENYRNGKIFLDVEM-RNLG 243
            SD SYLE QDM    GI R+VYLYA PK  I D+ V T L+E+    K+ + V++  +  
Sbjct: 215  SDASYLESQDMLRMTGIEREVYLYATPKQRIEDIQVVTHLNEDLTRAKLAIRVDIASHQP 274

Query: 244  EEEEKDLEVTLITPDG------DEKTLVKETVKPEDRVLSFAFDVKDPKKWSAETPHLYV 297
                 +LE  L+ P G      +++  +K   KP      F+  +  PK W+AE P+LY 
Sbjct: 275  GVRALELEARLLDPQGKPVAKANQRLSLKGDAKP-----VFSQTLISPKLWNAEMPNLYR 329

Query: 298  LKLKLGEDEKKV------NFGFRKIEIKDGTLLFNGKPLYIKGVNRHEFDPDRGHAVTVE 351
            L L L  ++ +         G RKI I++G L  N K + I+GV+RHE DP  GH V+ E
Sbjct: 330  LILTLKTEKGETLQVASQQIGVRKIAIENGQLKVNNKAITIRGVDRHETDPQTGHVVSRE 389

Query: 352  RMIQDIKLMKQHNINTVRTSHYPNQTKWYDLCDYFGLYVIDEANIESHGIDWDPEVTLAN 411
             M  DI+LMKQ+NIN VR+SHYPN   W  L D +GLYVIDEANIESH +  D +  L N
Sbjct: 390  TMELDIRLMKQNNINAVRSSHYPNHPYWLSLADRYGLYVIDEANIESHPLAIDDKTQLGN 449

Query: 412  RWEWEKAHFDRIKRMVERDKNHPSIIFWSLGNEAGDGVNFEKAALWIKKRDNTRLIHYEG 471
               W  AH  RI+RMVERDKNHPS+I WSLGNEAG+G  FE+   WIK+RD  R + YE 
Sbjct: 450  EMSWLPAHQARIERMVERDKNHPSVIIWSLGNEAGEGKLFERLYQWIKRRDPNRPVQYEP 509

Query: 472  TTRRGESYYVDVFSLMYPKMDILLEYASKKREKPFIMCEYAHAMGNSVGNLKDYWDVIEK 531
                GE+ Y D+ + MYP ++ + EYA +  ++P IM EYAHAMGNSVGNL+DYWDVIE 
Sbjct: 510  A---GEAPYTDIVAPMYPSIERIREYAERASDRPLIMIEYAHAMGNSVGNLQDYWDVIEA 566

Query: 532  YPYLHGGCIWDWVDQGIRKKDENGREFWAYGGDF-GDTPNDGNFCINGVVLPDRTPEPEL 590
            YP L GG IWDWVDQ +   ++ G+ +WAYG D+  D P DGNF  NG+V PDR P P L
Sbjct: 567  YPQLQGGFIWDWVDQALAFSNDLGQRYWAYGKDYHPDMPTDGNFLNNGLVDPDRNPHPHL 626

Query: 591  YEVKKVYQNVKIR----QVSKDTYEVENRYLFTNLEMFDGAWKIRKDGEVIEEKTFKI-F 645
             EVKKVYQ +K+R    +  K +  + N + F +       W ++KDG++I  K   +  
Sbjct: 627  SEVKKVYQPIKLRDFKVEGDKASVNLINGFDFASTSGLSLNWTLQKDGKIIASKRQAMPI 686

Query: 646  AEPGEKRLLKIPLPEMDD----SEYFLEISFSLSEDTPWAEKGHVVAWEQFLLKAPAFEK 701
              PGE+  + + LP         EY L +   +    P       +A+EQF L  P F  
Sbjct: 687  LSPGEQARVSLTLPGKQSLSAPFEYHLLLEVLVDTPRPLLPSDLRIAFEQFAL--PRFGT 744

Query: 702  KSI----SDGVSLREDGKHLTVEAKDTVYVFSKLTGLLEQILHRRKKILKSPVVPNFWRV 757
            K+      +   + ED     + + +  Y F K +G L QI    +  LK+P++ NFWR 
Sbjct: 745  KAAYQVKKNQAKISEDSGSYRLTSGELSYEFDKRSGWLTQIYQEGEPQLKAPLMANFWRA 804

Query: 758  PTDNDIGNRMPQRLAIWKRASKERKLFKMHWKKEENRVSVHSVFQLPGNSWVYTTYTVFG 817
            PTDND+GN+MP     W+ A+ E ++  +        +++       G S + T Y++  
Sbjct: 805  PTDNDLGNQMPDWAGAWQDAATELEVTAIDADLALG-LTISQTHAEKGFS-LRTRYSLDN 862

Query: 818  NGDVLVDLSLIPA-EDVPEIPRIGFQFTVPEEFGTVEWYGRGPHETYWDRKESGLFARYR 876
             G ++VD   IP  + + ++PR GF   +  E   + ++GRGP ETY DR+       Y 
Sbjct: 863  AGRLMVDSQFIPGNKPLADLPRFGFSTRLGFEHRYLSYFGRGPEETYADRQSGNPLGWYA 922

Query: 877  KAVGEMMHRYVRPQETGNRSDVRWFALSD--GETKLFVSG--------------MPQIDF 920
              + +  HRY RPQETG R+ VR+ A++D  G+  L ++               +  +  
Sbjct: 923  LPIEQTYHRYPRPQETGQRTQVRYAAVTDQRGQGWLAIANQAHAGEQDRKEADEVATLQT 982

Query: 921  SVWPFSMEDLE----------------RVQHISELPERDFVTVNVDFRQMGLGGDDSWGA 964
            S+WPF+  D++                   H +E+P R+FVT N+D+RQMG+GGD SWG 
Sbjct: 983  SLWPFAQADIDFRRGDAQDSASGLVAVTRNHGAEIPLREFVTWNIDYRQMGVGGDTSWGR 1042

Query: 965  MPHLEYRLLPKPYRFSFRM 983
              H  YR+  +P RF F +
Sbjct: 1043 PVHGPYRIKAEPIRFGFTL 1061


Lambda     K      H
   0.319    0.139    0.438 

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: 3321
Number of extensions: 168
Number of successful extensions: 9
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: 1087
Length of database: 1076
Length adjustment: 46
Effective length of query: 1041
Effective length of database: 1030
Effective search space:  1072230
Effective search space used:  1072230
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 (21.7 bits)
S2: 58 (26.9 bits)

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

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

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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