GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacZ in Flavobacterium glycines Gm-149

Align β-galactosidase (BgalB) (EC 3.2.1.23) (characterized)
to candidate WP_066328166.1 BLR17_RS02220 DUF4981 domain-containing protein

Query= CAZy::AAC24219.1
         (1085 letters)



>NCBI__GCF_900100165.1:WP_066328166.1
          Length = 1101

 Score =  671 bits (1730), Expect = 0.0
 Identities = 393/1043 (37%), Positives = 563/1043 (53%), Gaps = 79/1043 (7%)

Query: 5    WENPQLVSEGTEKPHASFIPYL---NPFTGEWEYPDDFILLNGNWKFFFAKNPFEVPENF 61
            WENP + S   E   A+   Y    +   G         +LNG+W F FAKN  E P++F
Sbjct: 49   WENPMITSMNREPARATAYSYATVADALEGN-RNKSRIKVLNGDWDFKFAKNFQEAPQDF 107

Query: 62   FLEGFDDTNWDEIEVPSNWEMKGYGKPIYTNVVYPFEP-NPPFVPKDDNPTGIYRRWVEV 120
            +  G     WD+I VPSNWEMKGYG  IY + VY F P NPPFVP+DDNP G Y+R   V
Sbjct: 108  YKNGVK--GWDKIAVPSNWEMKGYGMAIYKSAVYSFRPVNPPFVPQDDNPVGSYQRKFTV 165

Query: 121  PEEWFEKEIFLHFEGVRSFFYLWVNGKRMGFSKDSCTPAEFRVTDVLKPGKNLICVEVLK 180
            PE W    + LHF GV S F +W+NG+ +G+ +DSC  +EF +T  LK G+N++ V V +
Sbjct: 166  PENWDGMTVSLHFGGVSSAFQVWINGEFVGYGEDSCNSSEFNITPYLKKGENILSVRVFR 225

Query: 181  WSDGSYLEDQDMWWFAGIYRDVYLYALSKFHVRDIFVRTDLDEDYRDGKIFLDVELRNLG 240
            +SDGSYLEDQD W  +GI R+VY+ A  K  + D F +T LD+ Y+D    L   L N  
Sbjct: 226  YSDGSYLEDQDHWRLSGIQREVYIMAEPKLRIADFFYQTKLDKKYQDAVFQLRPRLDNQT 285

Query: 241  EE--KEKDLIITLTDPQGKEM----------TLVEERVGPKNETLSFVF---EVKDPKKW 285
             +  K     + L D Q K +           ++ E V P+ + + F F    +K+P KW
Sbjct: 286  GDTIKNHTFEVQLYDAQNKPLFEKDLSRKAIDIISE-VSPRLDKVRFGFFQETIKNPLKW 344

Query: 286  SAETPHLYVLKVELGEDE------KKVNFGFKKVEV--KDGRLLFNGKPLYIKGVNRHEF 337
            SAE P+LY L + L   +      K    GF+ +E   ++G++L NGK  Y+ GVN H  
Sbjct: 345  SAEKPNLYTLVMILKNPDGSISEVKTCKLGFRSIEFSKENGKMLINGKETYVYGVNHHGH 404

Query: 338  DPDRGHAVTVERMIQDIKLMKQHNINTVRTSHYPNQTKWYDLCDYYGLYVIDEANIESHG 397
             P RG AV  + + +D+KLMK++N N VRTSH+P    +Y+LCD YGL V+DEAN+E+HG
Sbjct: 405  HPSRGEAVNHQDLEEDVKLMKKYNFNFVRTSHFPEDPYFYELCDKYGLMVMDEANLETHG 464

Query: 398  IGEAPEVTLANRPEWEKAHLDRIKRMVERDKNHPSIIFWSLGNEAGDGMNFEKAALWIKE 457
            +G      L+N  +W  A+L+R+ RMV RDKNHPS++ WSLGNEAG G N    A W  +
Sbjct: 465  LGG----FLSNDQQWTHAYLERMTRMVHRDKNHPSVVMWSLGNEAGKGPNHAAMAGWTHD 520

Query: 458  RDNTRLVHYE--------------------GTTRRGESY-------YVDVFSLMYPKIDV 490
             D TR VHYE                     T      Y       YVDV S  YP +  
Sbjct: 521  YDITRPVHYEPAQGNPRLDGYIDPLDPRYPKTVDHSHRYENPQDEPYVDVVSRFYPGVFT 580

Query: 491  LLEYASRKRE-KPFIMCEYAHAMGNSVGNLKDYWDVIEKYPYLHGGCIWDWVDQGIRKKD 549
                  +K++ +P +  EY+H+MGNS GNLK+ WD     P + GGCIWD  DQG+ +KD
Sbjct: 581  PKFLVDQKKDTRPILFVEYSHSMGNSTGNLKELWDEFRNTPRVIGGCIWDLKDQGLLRKD 640

Query: 550  -ENGKEFWAYGGDFGDEPNDKNFCCNGVVLPDRTPEPELYEVKKFYQNIKVRQIAKDTYE 608
             + G+E+  YGGDFG++ +D NF  NG+V  D   +  +YE K  YQ             
Sbjct: 641  AKTGQEYLGYGGDFGEKKHDGNFNINGMVSADGRAKAAMYENKWIYQPAVSSLSTDFKLN 700

Query: 609  VENGYLFTDLEMFDGTWRIRKDGEVVREERFK-LSARPGEKKILKIP--LP-EMEDSEYF 664
            + N  +  +L  F    +I ++G ++++   + +    G   +L +   LP   +DSEYF
Sbjct: 701  IHNRQVVQNLRDFIPVIQILENGNLIKQFVLQPIDIPAGGDYVLDVKKYLPNRKKDSEYF 760

Query: 665  LEICFSLSEDTLWAKKGHVVAWEQFLI-KPPSFEKTVVRESVDLSEDGRHLFVRSKDTEL 723
            L I F L++D  WA KG+ VA +QFL+ K         ++  +L E      +  +D  +
Sbjct: 761  LNIEFQLAKDEFWASKGYAVATDQFLLQKKTEVVLAEAKQKSNLQETKEAYAINGRDFSI 820

Query: 724  VFSKFTGLLKRIVYRGRNILTGSIVPNFWRVPTDND-VGNKMPERLSIWKRASKERKLFK 782
              +K  G L   VY+G+  +   ++PNF R  TDND  G K  + L  W  A    K  K
Sbjct: 821  KINKANGALSSYVYKGKEQIKADLLPNFTRALTDNDRKGWKPHKLLKQWYLAKPMLKNIK 880

Query: 783  MFFWKKEENSVSVQSVYQ-VPGNSWVYLTYTIFGNGDILVDLSLIPAEGVPEIPRIGLQF 841
            M   ++    + + S Y+ +  ++ V + Y I  NG + V+  L     +P IPRIG+Q 
Sbjct: 881  M---EQSAGDIKISSDYEIIKDSAAVKVVYNINANGIVKVNYQLNANPKLPNIPRIGMQL 937

Query: 842  AVPGDFRFVEWYGRGPHETYWDRKESGLFARYRRTVQDMIHRYVRPQETGNRSDVRWFAL 901
             +  DF  + WYG+G  E Y DR       RY   +   I  YV PQE  NR++VRW A 
Sbjct: 938  GINQDFGQISWYGKGELENYCDRSFGFTVGRYSLPIDKFIEPYVMPQENANRTEVRWMAF 997

Query: 902  SDGRVN---LFVSGMPVVDFSVWPFSMEDLEKADHVNELPERDFVTVNVDYRQMGLGGDD 958
            ++   +   + V+   V++ S WP++ ++L+ A H  +L    F+TVNVD +QMG+GG+D
Sbjct: 998  TNPTKSSGLIVVNEDKVLNMSAWPYTQQNLDDAKHTYDLVNPGFLTVNVDLKQMGVGGND 1057

Query: 959  SWG--AQPHLEYRLLPEPYRFSF 979
            SW   + P  +Y++    Y++SF
Sbjct: 1058 SWSPVSAPMEKYQIPSGDYQYSF 1080


Lambda     K      H
   0.320    0.140    0.440 

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: 3546
Number of extensions: 219
Number of successful extensions: 13
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: 1085
Length of database: 1101
Length adjustment: 46
Effective length of query: 1039
Effective length of database: 1055
Effective search space:  1096145
Effective search space used:  1096145
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: 58 (26.9 bits)

This GapMind analysis is from Sep 24 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:

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:

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:

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:

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