GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Smeli:SM_b20894 SM_b20894 sugar uptake ABC
           transporter ATP-binding protein
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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