GapMind for catabolism of small carbon sources

 

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

Align β-galactosidase (Gal4214-1) (EC 3.2.1.23) (characterized)
to candidate WP_066328293.1 BLR17_RS01685 DUF4981 domain-containing protein

Query= CAZy::AAX48919.1
         (1046 letters)



>NCBI__GCF_900100165.1:WP_066328293.1
          Length = 1039

 Score = 1031 bits (2665), Expect = 0.0
 Identities = 506/1041 (48%), Positives = 694/1041 (66%), Gaps = 24/1041 (2%)

Query: 15   FISIIVFAQEK---PSRNDWENPEVFQINREPARAAFLPFADEASAIADDYTRSPWYMSL 71
            F+++++F   +      NDWENP++    +   R++FL +++ A    +D  +S  Y SL
Sbjct: 5    FLALVLFLGAQINFAQNNDWENPQLLDRGKIEGRSSFLLYSNHAELKRNDPRKSVLYQSL 64

Query: 72   DGKWKFNWSPTPDERPKDFFNTDFNTTTWKEIGVPSNWELVGYGIPIYTNITYPFVKNPP 131
            +G WKFN    P +RP D+++ + + + W  I VPSNWE+ GY IPIYTNITYPF KNPP
Sbjct: 65   NGDWKFNIVKNPIQRPLDYYSENLDDSKWNVIKVPSNWEMQGYDIPIYTNITYPFPKNPP 124

Query: 132  FIDHADNPVGSYRRTFELPENWDGRRVYLHFEGGTSAMYVWINGEKVGYSQNTKSPTEFD 191
            FI    NPV SYRRTF + + W  + + LHF   T    V++NG++VG ++ +K+P EF+
Sbjct: 125  FIGGDYNPVASYRRTFTIADFWKDKEIILHFGSITGYAKVFLNGKEVGMTKASKTPAEFN 184

Query: 192  ITKYVKVGKNQVAVEVYRWSDGSYLEDQDFWRLSGIDRSVYLYSTANTRIADFFARPDLD 251
            IT ++K G N +AV+V+RW DGSYLEDQDFWRLSGI+R VYL +   T + D+F + DLD
Sbjct: 185  ITSFLKKGDNLIAVQVFRWHDGSYLEDQDFWRLSGIERDVYLQAMPKTTVWDYFVKSDLD 244

Query: 252  TSYKNGSLSVDIKLKNANSVAKNNQTVEAKLVDAAGKEVFIKTIKINLGANTVSSTTFEQ 311
              YKNG  ++D+ LK+  +    N  V+ +L D  GK VF ++ K+N     +S   F++
Sbjct: 245  YQYKNGIFNLDVTLKSFENNKIKNPAVKVELFDKDGKVVFSESKKVNSKEPKIS---FQK 301

Query: 312  MVKSPKLWNNETPNLYTLVLTLKDENGKFVETVATSIGFRKVELKNGQLLVNGIRIMVHG 371
             +++ K WN ETPNLY   +TL D  G   E ++   GFRKVE+KN QLLVNG  ++V G
Sbjct: 302  TIENVKQWNAETPNLYRYTITLLDSKGNVFEVISKKTGFRKVEIKNAQLLVNGKAVLVKG 361

Query: 372  VNIHEHNPKTGHYQDEATMMKDIKLMKQLNINAVRCSHYPNNLLWVKLCNKYGLFLVDEA 431
            VNIHEH+   GH  ++  M KD++LMK+ NIN++R  HYP++  +  LC++YG ++VDEA
Sbjct: 362  VNIHEHDDVNGHVPNKDLMKKDLQLMKEFNINSIRMCHYPHDTQFYDLCDEYGFYVVDEA 421

Query: 432  NIETHGMGAELQGSFDKTKHPAYLPEWKAAHMDRIYSLVERDKNQPSIILWSLGNECGNG 491
            NIETHGMGAE Q  FD+ KHPAYLPEW  AH+DRI  +   DKN PSII+WSLGNECGNG
Sbjct: 422  NIETHGMGAEWQNWFDQKKHPAYLPEWAPAHLDRIKRMFAFDKNHPSIIIWSLGNECGNG 481

Query: 492  PVFHEAYNWIKNRDKTRLVQFEQAGEQENTDVVCPMYPSMEYMKEYANRKDVKRPFIMCE 551
            PVF++AYNW+K  D TRLVQFEQAGE +NTD+VCPMYPS++ MK YA+ K   RP+IMCE
Sbjct: 482  PVFYDAYNWLKQADSTRLVQFEQAGENKNTDIVCPMYPSIKSMKTYADAKK-DRPYIMCE 540

Query: 552  YSHAMGNSNGNFQEYWDIIHSSTNMQGGFIWDWVDQGFEETDEAGRKYWAYGGDMGGQNY 611
            YSHAMGNS+GNFQEYWDIIH+S +MQGGFIWDWVDQG +  +E G ++WAYGGD+G  + 
Sbjct: 541  YSHAMGNSSGNFQEYWDIIHASKHMQGGFIWDWVDQGMKTKNEKGVEFWAYGGDLGSAHL 600

Query: 612  TNDQNFCHNGLVWPDRTPHPGAFEVKKVYQDILFKGVNLDKGIIEVENGFGYTNLDKYLF 671
             ND+NFC NGLV  +R PHPG FEVKKVYQDI F+  N D  ++ V+N F +TNL  Y F
Sbjct: 601  HNDENFCSNGLVSANRIPHPGLFEVKKVYQDIQFQLKN-DTDLL-VKNYFNFTNLSNYTF 658

Query: 672  KFEVLKNGLVIKSGVINIRLAPQSKKQIQIELPKLTTEDGVEYLLNVFAYTKEGTELLPQ 731
            K+E++KNGL + SG  N+ + P+  K+I++     T + G EY LNVFA +K  T L+ +
Sbjct: 659  KWELIKNGLKVNSGEFNLDVNPEETKEIKLNYG--TLDAGAEYFLNVFAVSKYDTPLVVK 716

Query: 732  NFEIAREQFSIGESNYFVKVAKASTNP-----IVKDSQDAITLSANGVEVTINKKTGLMQ 786
              E AREQF+IG+ +YF     AS +P      VK   + ++     +    + K G + 
Sbjct: 717  GHEFAREQFAIGQGDYFKNNVLASKSPSKFKYAVKG--NVLSFETENIMGEFDLKNGELV 774

Query: 787  KY--TSGEENYFNQMPVPNFWRAPTDNDFGNYMQVNSNVWRTVGRFSSLDSIEVKEVSTQ 844
            KY   +      +  P P FWRAPTDNDFG+ MQ    +WR   +  ++ S+ + + S++
Sbjct: 775  KYGLKNDPSTIISGFPTPYFWRAPTDNDFGSGMQNKLVIWREAHKNPTVVSVNLDKKSSE 834

Query: 845  TTVVAHLF-LKDIASTYTITYSMDADGSLTLQNSFKAGEMALSEMPRFGMLFSLKKELDN 903
              +V  ++ L  +   Y++ Y +  +GS+ +  S       L E+PRFGM   L    DN
Sbjct: 835  GVLVKVVYKLAQVEVPYSVDYLIQNNGSVKITASVDMNGKELPELPRFGMRMKLNGAYDN 894

Query: 904  FSYYGRGPWENYQDRNTSSLKGIYESKVADQYV-PYTRPQENGYKTDIRWITLTNSSGNG 962
             SYYGRGPWENY DRNT+S  G+Y  KV +Q+   Y RPQE+GYKTD+RW+ L +S G G
Sbjct: 895  LSYYGRGPWENYADRNTASFMGVYSDKVINQFTRNYIRPQESGYKTDVRWLVLNDSKGKG 954

Query: 963  IEILGLQPLGVSALNNYPEDFDPGLTKKQQHTN--DITPRDEVIICVDLAQRGLGGDNSW 1020
            ++I G+QP+G S LN   ED DPG  K Q+H +  D+  ++ V + +D  QRG+GGD+SW
Sbjct: 955  LKIEGVQPIGFSTLNIPTEDLDPGKRKSQRHPSDLDLDSKEVVYLHLDYKQRGVGGDDSW 1014

Query: 1021 GAMPHEQYQLRNKAYSYGFVI 1041
            G++PH+ Y+L +K YSY +VI
Sbjct: 1015 GSLPHDSYRLLDKKYSYSYVI 1035


Lambda     K      H
   0.316    0.134    0.410 

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: 3448
Number of extensions: 180
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: 1046
Length of database: 1039
Length adjustment: 45
Effective length of query: 1001
Effective length of database: 994
Effective search space:   994994
Effective search space used:   994994
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 58 (26.9 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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