GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Sinorhizobium meliloti 1021

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate SM_b20894 SM_b20894 sugar uptake ABC transporter ATP-binding protein

Query= TCDB::O05176
         (512 letters)



>FitnessBrowser__Smeli:SM_b20894
          Length = 506

 Score =  750 bits (1937), Expect = 0.0
 Identities = 378/476 (79%), Positives = 426/476 (89%)

Query: 36  LVGENGAGKSTLMKVLSGVYPAGTYEGEIHYEGAVRNFRAINDSEDIGIIIIHQELALVP 95
           L G+    KSTLMKVLSGVYPAGTYEGEIHY+G +R F  I+DSE++GIIIIHQELALVP
Sbjct: 31  LSGKTAPAKSTLMKVLSGVYPAGTYEGEIHYDGELRQFSTISDSEELGIIIIHQELALVP 90

Query: 96  LLSIAENIFLGNEVASNGVISWQQTFNRTRELLKKVGLKESPETLITDIGVGKQQLVEIA 155
           LLSIAENIFLGNEVA  GVI W QTF RT+ELLKKVGL ESP TLITDIGVGKQQLVEIA
Sbjct: 91  LLSIAENIFLGNEVAEKGVIHWPQTFARTQELLKKVGLNESPATLITDIGVGKQQLVEIA 150

Query: 156 KALSKSVKLLILDEPTASLNESDSEALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITV 215
           KALSK V+LLILDEPTASLNE+DS+ALL LLMEFR+QGMTSIII+HKLNE++KVADQIT+
Sbjct: 151 KALSKKVRLLILDEPTASLNENDSDALLKLLMEFRSQGMTSIIISHKLNEIKKVADQITI 210

Query: 216 LRDGMTVKTLDCHQEEISEDVIIRNMVGRDLEDRYPPRDVPIGETILEVKNWNAYHQQHR 275
           LRDG TV+TLDCH+E+ISED II  MVGR +EDRYPPR+  IG+T+LEVKNWN YHQ HR
Sbjct: 211 LRDGGTVETLDCHKEDISEDRIINGMVGRAMEDRYPPREPKIGDTLLEVKNWNVYHQHHR 270

Query: 276 DRQVLHDINVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTV 335
           DRQ LHD++  VR GEVVGIAGLMGAGRTE AMSVFGKS+GH+ITG+V + G+PVDVST+
Sbjct: 271 DRQFLHDVSFKVRAGEVVGIAGLMGAGRTETAMSVFGKSWGHKITGEVTMHGRPVDVSTI 330

Query: 336 RKAIDAGLAYVTEDRKHLGLVLNDNILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRL 395
            KAI AGLAYVTEDRK LGLVL +NI+HNTTLANL  V+   +ID+ KE KVA+++R++L
Sbjct: 331 PKAIKAGLAYVTEDRKQLGLVLINNIMHNTTLANLHAVASNGVIDERKERKVAAEYRSKL 390

Query: 396 RIRSSGIFQETVNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLA 455
           RIRS  I+QETVNLSGGNQQKVVLSKWLF+NP+VLILDEPTRGID+GAKYEIYTIINQLA
Sbjct: 391 RIRSHSIYQETVNLSGGNQQKVVLSKWLFTNPEVLILDEPTRGIDIGAKYEIYTIINQLA 450

Query: 456 ADGKGVLMISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQESIMRAIMRSGEKN 511
           A+GKG+LMISSEMPELLG CDRIYVMNEGR+VAEL K EASQESIMRAIMRSGEK+
Sbjct: 451 AEGKGILMISSEMPELLGTCDRIYVMNEGRMVAELSKEEASQESIMRAIMRSGEKH 506



 Score = 73.2 bits (178), Expect = 2e-17
 Identities = 64/248 (25%), Positives = 120/248 (48%), Gaps = 11/248 (4%)

Query: 1   MANTILEMRNIT---KTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPA 57
           + +T+LE++N     +     + L +V+ KV+ GE+  + G  GAG++     + G    
Sbjct: 252 IGDTLLEVKNWNVYHQHHRDRQFLHDVSFKVRAGEVVGIAGLMGAGRTETAMSVFGKSWG 311

Query: 58  GTYEGEIHYEGAVRNFRAINDSEDIGIIII---HQELALVPLLSIAENIFLGN--EVASN 112
               GE+   G   +   I  +   G+  +    ++L LV + +I  N  L N   VASN
Sbjct: 312 HKITGEVTMHGRPVDVSTIPKAIKAGLAYVTEDRKQLGLVLINNIMHNTTLANLHAVASN 371

Query: 113 GVISWQQTFNRTRELLKKVGLK-ESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPT 171
           GVI  ++      E   K+ ++  S      ++  G QQ V ++K L  + ++LILDEPT
Sbjct: 372 GVIDERKERKVAAEYRSKLRIRSHSIYQETVNLSGGNQQKVVLSKWLFTNPEVLILDEPT 431

Query: 172 ASLNESDSEALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEE 231
             ++      +  ++ +   +G   ++I+ ++ E+    D+I V+ +G  V  L   +EE
Sbjct: 432 RGIDIGAKYEIYTIINQLAAEGKGILMISSEMPELLGTCDRIYVMNEGRMVAELS--KEE 489

Query: 232 ISEDVIIR 239
            S++ I+R
Sbjct: 490 ASQESIMR 497


Lambda     K      H
   0.316    0.135    0.374 

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: 843
Number of extensions: 24
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 512
Length of database: 506
Length adjustment: 34
Effective length of query: 478
Effective length of database: 472
Effective search space:   225616
Effective search space used:   225616
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: 52 (24.6 bits)

This GapMind analysis is from Sep 17 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