GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malI in Dyella japonica UNC79MFTsu3.2

Align The maltose/maltooligosaccharide transporter, MalI (541 aas) (characterized)
to candidate N515DRAFT_3387 N515DRAFT_3387 maltose/moltooligosaccharide transporter

Query= TCDB::Q9A612
         (541 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3387
          Length = 497

 Score =  544 bits (1402), Expect = e-159
 Identities = 286/493 (58%), Positives = 348/493 (70%), Gaps = 17/493 (3%)

Query: 44  LSFLQIWNMCFGFFGIQIGFGLQNANTSRIFQSLGVDVNHLAILWIAAPATGLLVQPIIG 103
           L+F QIWNMCFGF GIQ GF LQNAN SRIFQ+LG DV  + +LW+AAP +GL+VQPI+G
Sbjct: 12  LTFWQIWNMCFGFLGIQFGFALQNANVSRIFQTLGADVGDIPMLWVAAPLSGLIVQPIVG 71

Query: 104 HFSDKTWGRFGRRRPYFFWGAILTTLALLVMPNSPTLWVAAAALWIMDASINITMEPFRA 163
           + SD+TW   GRRRPYF  GA+L TL LL MPN+P LWVAA  LWI+DASIN++MEPFRA
Sbjct: 72  YLSDRTWTGLGRRRPYFLVGAVLATLGLLWMPNAPALWVAAGLLWILDASINVSMEPFRA 131

Query: 164 FVGDNLPDEQRATGYAMQSFFIGLGAVFASALPWMLTNWFDVANTAPAGQVPDSVRIAFY 223
           FVGD LP  QR  GYAMQSFFIGLGAV ASALPW+L     V+N      +PD+VR AFY
Sbjct: 132 FVGDQLPPRQRPLGYAMQSFFIGLGAVVASALPWILER-LGVSNAPGVSGIPDTVRYAFY 190

Query: 224 TGGAGLLLAVLWTVFTTREYSPEQLTAFEKAEREIAGLGLHEEPEPSVNAYIALGVGGVL 283
            GGA LL +VLWTV +TREY PE L AF+ A  E   +       P+ + +   G+  + 
Sbjct: 191 AGGAVLLGSVLWTVCSTREYPPETLAAFDHAPVEETAVD-----RPAASRW---GLLWLA 242

Query: 284 LGAALALIVWGAGLEKELYVLAGLLFAFGLAGVAGARFKRIGRTDNG--FSEVLADVFRM 341
            G AL  +V    LEKELY+L G +  FG+A         +GRT +    ++VL D+F M
Sbjct: 243 AGLALTAVVAFMRLEKELYLLTGGMSVFGVA------LLWLGRTASRGPAAQVLGDLFGM 296

Query: 342 PKTMRQLAVVQFFSWFGLFAMWIYTTPAVATVHFGAVDASSKAYNEGADWVGVLFAVYNG 401
           P+ MR+LA VQ FSWF LFAMWIYTT  V  VH+G+ D  S AYNEGA+WVGVLFA YNG
Sbjct: 297 PEAMRRLAWVQLFSWFALFAMWIYTTAGVTQVHYGSSDPHSAAYNEGANWVGVLFAAYNG 356

Query: 402 VAALAALVIPLMVKVTSRRVSHAVCLGLGALGLLSFLVIRDPGLLWIGMVGVGFAWSSIL 461
            AALAA+VIP MV+    R+SH V + LG  G LSFL+I DP  L + MVGVGFAW+SIL
Sbjct: 357 FAALAAIVIPWMVRRWGIRISHLVNVWLGGAGFLSFLLIHDPRWLLLSMVGVGFAWASIL 416

Query: 462 STPYSILAGALPARKMGVYMGIFNVFIVVPQLLAATLLGLMLKTFFGNQSIFALVLGALS 521
           S PY++L+  LPA KMGVYMGIFN F+V+PQLLAA++LGL+L+ FF  Q I+ALVLG  S
Sbjct: 417 SLPYALLSDNLPAHKMGVYMGIFNFFVVIPQLLAASVLGLLLRAFFHGQPIYALVLGGAS 476

Query: 522 FALAAAATFLVRD 534
             ++      VR+
Sbjct: 477 LFVSGLCVLRVRE 489


Lambda     K      H
   0.327    0.140    0.437 

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: 934
Number of extensions: 53
Number of successful extensions: 4
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: 541
Length of database: 497
Length adjustment: 35
Effective length of query: 506
Effective length of database: 462
Effective search space:   233772
Effective search space used:   233772
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 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