Alignments for a candidate for susB in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for susB in Echinicola vietnamensis KMM 6221, DSM 17526

Align α-glucosidase (BT0339;BT_0339) (EC 3.2.1.20) (characterized)
to candidate Echvi_1677 Echvi_1677 Alpha-glucosidases, family 31 of glycosyl hydrolases

Query= CAZy::AAO75446.1
         (748 letters)



>FitnessBrowser__Cola:Echvi_1677
          Length = 756

 Score =  997 bits (2578), Expect = 0.0
 Identities = 459/748 (61%), Positives = 569/748 (76%), Gaps = 3/748 (0%)

Query: 1   MKPTNYHLFDFLDFDTELLR--DESLWKACKPTAVYEKDGDICVTVPFQKQLLANDMVAD 58
           MK TNY LFDFLDFD E L    + LW+A +P A+   D  I V VPF  Q  A D+  D
Sbjct: 1   MKQTNYQLFDFLDFDPERLEVSADRLWRAGRPLAIESFDKGIIVHVPFHCQKPAVDIQPD 60

Query: 59  TAVPREEYTLIIRQYNIGITRLFLGFGEYELTDQSEMLQFSERIRRVPLSVEKQGGKWIL 118
           + V  + + + IR +   + R+    G+ + +  S ML+ ++ +  VPLS+EK   +W++
Sbjct: 61  SEVAPQSFEVHIRAFGERVLRVTAELGQ-KASKASPMLEIADDLEEVPLSIEKADNEWVI 119

Query: 119 FTQDGTKRAVINVEEPALDRWSELLPDPQETLDITLYPDGKREIRLAAYDHFSPPRYDGL 178
                  RA+I++ +P  D WS+LLP P+     T +PDGK+ ++L  +D F P R D +
Sbjct: 120 KDDRQVVRAIIDLTDPVTDWWSDLLPPPEPVFQATFFPDGKKAVKLNGHDQFFPARVDAM 179

Query: 179 PIAFCKRTGKKERATLSFESRPDECFAGTGERFFKMDLSGQTLFLKNQDGQGVNNRRTYK 238
            +A         +ATLSF ++PDE F GTGERF KMDLSG+T  LKNQDGQGVNNRRTYK
Sbjct: 180 GLAMISENEIPTKATLSFAAQPDEKFVGTGERFTKMDLSGRTFQLKNQDGQGVNNRRTYK 239

Query: 239 NIPFYLSSRMYGTFYHTCAHSKLSLAGHSTRSVQFLSDQAMLDAFVIAGDTMEEILRGYR 298
           NIPFYLSS MYG F HT A+ K+SLA HSTRSVQ L ++ + D F++ GD   EIL  YR
Sbjct: 240 NIPFYLSSEMYGLFLHTSAYGKISLADHSTRSVQLLVEEPLADVFLLGGDNPHEILHEYR 299

Query: 299 DLTGYPSMPPLWSFGVWMSRMTYFSADEVNEICDRMRAEHYPCDVIHLDTGWFRTDWLCE 358
            LTG+P+MPPLW+FGVWMSRMTYFSA+EV  ICDR+RAE +PCDVIHLDTGWF TDWLCE
Sbjct: 300 RLTGFPAMPPLWTFGVWMSRMTYFSAEEVEGICDRLRAERFPCDVIHLDTGWFETDWLCE 359

Query: 359 WKFNEERFPDPKGFIQRLKKNGYRVSLWQLPYVAEDAEQIEEAKANEYIAPLTKQQDTDG 418
           WKFN +RFP PKGF+Q+LKK GYRVSLWQ+PY+A +A Q EEAKAN YI PL + +   G
Sbjct: 360 WKFNTDRFPHPKGFVQKLKKQGYRVSLWQMPYIAANAMQHEEAKANNYIGPLKESKVQGG 419

Query: 419 SNFSALDYAGTIDFTYPKATEWYKGLLKQLLDMGVTCIKTDFGENIHMDAVYKGMKPELL 478
           SNFSALDYAGTIDFTYP A EWYKGLL++LL+MGVTCIKTDFGE IH+DA Y  M   LL
Sbjct: 420 SNFSALDYAGTIDFTYPAAVEWYKGLLRELLEMGVTCIKTDFGEEIHLDAAYHDMPAPLL 479

Query: 479 NNLYALLYQKAAYEITKEVTGDGIVWARAAWAGCQRYPLHWGGDSCSSWDGMAGSLKGGL 538
           NNLYALLYQKAA+E+T+EV G+G+VWARA WAGCQRYP+HWGGD+ +SWDGMAGSLKGGL
Sbjct: 480 NNLYALLYQKAAFEVTEEVAGEGVVWARAGWAGCQRYPIHWGGDAAASWDGMAGSLKGGL 539

Query: 539 HFGLSGFAFWSHDVPGFHTLPNFMNSIVAEDVYMRWTQFGVFTSHIRYHGTNKREPWHYP 598
           H GLSGF FWSHDVPGFH +PNFMNS++ +D+Y+RWTQFGVFTSHIRYHGT+KREP+ YP
Sbjct: 540 HLGLSGFGFWSHDVPGFHGVPNFMNSVIPDDLYVRWTQFGVFTSHIRYHGTSKREPYEYP 599

Query: 599 AIAPLVKKWWKLRYSLIPYIIEQSKLAVESGWPLLQALILHHPEDKLCWHIDDEYYFGND 658
           AIA +V+KWW+LRY L+PYI+EQS+ ++ SG P+L+A++LH P+D +CWH+DD+Y+FG D
Sbjct: 600 AIADVVRKWWELRYVLLPYILEQSQQSIRSGMPMLRAMLLHFPDDPMCWHLDDQYFFGED 659

Query: 659 FLVAPVMNSENRRDIYLPEGQWVNFFTGERLQGGRWLKEVYVPLEEMPVYVRENAVIPIY 718
           FLVAPVMNS N R +YLPEG WV+FFTG   +G +W+    +PLEEMPV+V++ A IPIY
Sbjct: 660 FLVAPVMNSGNARKVYLPEGSWVDFFTGTCQEGPKWVAMDPIPLEEMPVWVKQGASIPIY 719

Query: 719 PEEVNCTDEMDLGKSIALRIDHNYKGFW 746
           P  V+CTDEMD  K+  L ID  + G W
Sbjct: 720 PTSVSCTDEMDFKKTQPLVIDGGFNGIW 747


Lambda     K      H
   0.322    0.139    0.449 

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: 1909
Number of extensions: 88
Number of successful extensions: 3
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: 748
Length of database: 756
Length adjustment: 40
Effective length of query: 708
Effective length of database: 716
Effective search space:   506928
Effective search space used:   506928
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: 55 (25.8 bits)

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

Downloads

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