GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malI in Sphingopyxis indica DS15

Align The maltose/maltooligosaccharide transporter, MalI (541 aas) (characterized)
to candidate WP_089216658.1 CHB69_RS14150 MFS transporter

Query= TCDB::Q9A612
         (541 letters)



>NCBI__GCF_900188185.1:WP_089216658.1
          Length = 499

 Score =  483 bits (1244), Expect = e-141
 Identities = 248/493 (50%), Positives = 330/493 (66%), Gaps = 9/493 (1%)

Query: 39  MARQRLSFLQIWNMCFGFFGIQIGFGLQNANTSRIFQSLGVDVNHLAILWIAAPATGLLV 98
           M + R  F  +WN+ FGFFGIQIGF LQNAN SRIFQSLG D+  L  LW+AAP TGLLV
Sbjct: 1   MEKPRQGFAGLWNISFGFFGIQIGFALQNANMSRIFQSLGEDIEKLPGLWVAAPLTGLLV 60

Query: 99  QPIIGHFSDKTW-GRFGRRRPYFFWGAILTTLALLVMPNSPTLWVAAAALWIMDASINIT 157
           QP+IGH SD+TW GR GRRRPYF  GAIL  +AL  MP SP++W AA  LW++DAS+NI+
Sbjct: 61  QPVIGHLSDRTWLGRLGRRRPYFLAGAILAAIALFAMPESPSIWFAAVMLWLLDASLNIS 120

Query: 158 MEPFRAFVGDNLPDEQRATGYAMQSFFIGLGAVFASALPWMLTNWFDVANTAPAGQVPDS 217
           MEPFRAFVGD L  +Q + GYA+Q+ FIG GAV  S  P ++   F VAN AP GQ+P++
Sbjct: 121 MEPFRAFVGDMLRKDQHSAGYAVQTAFIGAGAVVGSLFPSVMEA-FGVANVAPPGQIPET 179

Query: 218 VRIAFYTGGAGLLLAVLWTVFTTREYSPEQLTAFEKAEREIAGLGLHEEPEPSVNAY-IA 276
           VR AF+ GGA LLL+VLWTV +T EY P ++ AFE A     G  +   P  ++ ++  A
Sbjct: 180 VRYAFWFGGAALLLSVLWTVVSTDEYDPARMAAFETA-----GDAVELPPMRALASHSYA 234

Query: 277 LGVGGVLLGAALALIVWGAGLEKELYVLAGLLFAFGLAGVAGARFKRIGRTDNGFSEVLA 336
              G +  G  +AL+    GL +E+ +L  LL  +GLA +      R G + N  S ++ 
Sbjct: 235 ASFGWIAAGVVVALVQIRLGLLREVLLLGALLAGYGLASMLAIALARRGSSTNMLSSIVG 294

Query: 337 DVFRMPKTMRQLAVVQFFSWFGLFAMWIYTTPAVATVHFGAVDASSKAYNEGADWVGVLF 396
           D   MP  M++LA+VQFFSW  LF MWI TTP VA  H+G  DA+S AY E A+WVG LF
Sbjct: 295 DFSGMPALMKRLAIVQFFSWSALFVMWINTTPIVAQYHYGTRDAASAAYQEAANWVGELF 354

Query: 397 AVYNGVAALAAL-VIPLMVKVTSRRVSHAVCLGLGALGLLSFLVIRDPGLLWIGMVGVGF 455
           A+YNGVAA+AAL ++P + +   +  +H   L  GA G  SF V+RDP  L +  + +G 
Sbjct: 355 AIYNGVAAIAALTLLPWLARRLGQARTHMTGLACGAAGYASFFVLRDPMHLIVSEIFIGI 414

Query: 456 AWSSILSTPYSILAGALPARKMGVYMGIFNVFIVVPQLLAATLLGLMLKTFFGNQSIFAL 515
            W+S+L+ PY+ILA +LP  K+GVYMG+FNVF+V+PQLL AT++G +++ FF  + I+ +
Sbjct: 415 FWASVLAMPYAILASSLPQAKLGVYMGLFNVFVVIPQLLVATVMGSVMQAFFPGEPIYTM 474

Query: 516 VLGALSFALAAAA 528
              A++  +A  A
Sbjct: 475 AFAAVTLMVAMIA 487


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: 770
Number of extensions: 37
Number of successful extensions: 5
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: 499
Length adjustment: 35
Effective length of query: 506
Effective length of database: 464
Effective search space:   234784
Effective search space used:   234784
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 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