Alignments for a candidate for PS417_12065 in Skermanella stibiiresistens SB22

GapMind for catabolism of small carbon sources

Alignments for a candidate for PS417_12065 in Skermanella stibiiresistens SB22

Align D-ribose transporter ATP-binding protein; SubName: Full=Putative xylitol transport system ATP-binding protein; SubName: Full=Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_037450705.1 N825_RS10360 sugar ABC transporter ATP-binding protein

Query= uniprot:A0A1N7TX47
         (495 letters)



>NCBI__GCF_000576635.1:WP_037450705.1
          Length = 510

 Score =  333 bits (855), Expect = 6e-96
 Identities = 182/491 (37%), Positives = 289/491 (58%), Gaps = 7/491 (1%)

Query: 6   LLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILL 65
           LL+   + K++AG+ AL    L+LRAG +HAL G NGAGKST +  + G+ +RDAG++ L
Sbjct: 11  LLEVRGLTKSFAGIRALDGVDLTLRAGEIHALLGENGAGKSTLIKTITGVLRRDAGTVSL 70

Query: 66  NGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRAGCIVDNKALNRRTR 125
           +G+P+  +   EA  AGIA + QE+  +P ++VA+N++LGR+P R G + + +   RR R
Sbjct: 71  DGSPIAPHSAEEAATAGIATVYQEVSLLPNLSVAQNLFLGRQPTRFGFVREGET-RRRAR 129

Query: 126 ELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFKA 185
            LL     D+D T+P+   SVA   L  IA+A     +V+I+DEPT+++  +E + LF  
Sbjct: 130 LLLRDFGLDIDVTAPLDSYSVAVRHLTAIARAVDMSARVLILDEPTASLDANEVEILFTV 189

Query: 186 IRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQELT 245
           +R+L A+G GIV+V+H L ++  + D  ++ R+G  V+    A++ R  LVR ++G+EL 
Sbjct: 190 MRKLAARGIGIVFVTHFLDQVYAVTDRITVLRNGRLVDERLTAELPRMDLVRMMLGRELV 249

Query: 246 RIDHKVGRECAANTCLQ-----VDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLN 300
                  RE  + T +       +N  ++G      L +R GE++G+ GL+GSGR+E   
Sbjct: 250 EAT-ATHREAVSPTAMSEPYAVFENFGKSGYVAPFDLTVRGGEVVGLAGLLGSGRTETTR 308

Query: 301 CIYGLTVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAY 360
            ++G+  AD G+VT+ GKP  I  P   +  G+    E+RK  G+V   ++  NI L+  
Sbjct: 309 LVFGVEKADQGTVTIAGKPASISSPSEAVGHGLGYCPEERKTEGIVADLTVRENIVLALQ 368

Query: 361 KRLSSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCL 420
            R      ++ R++ ++A   ++ L I+    E P+  +SGGNQQK +LA+ L+TEP  L
Sbjct: 369 ARRGVMRPLSRREQDEIANKFIRLLDIRPPDPERPIGLLSGGNQQKALLARWLATEPRLL 428

Query: 421 LCDEPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLVTIS 480
           + DEPTRGID GA  EI  L+ Q    G A +VVSSE  E++  +DR+ V +    V   
Sbjct: 429 ILDEPTRGIDVGAHAEIIRLIRQLCADGMALLVVSSELEEIVAYADRVIVLRDRAHVACL 488

Query: 481 TDTALSQEALL 491
              A+++  +L
Sbjct: 489 EGDAVNEPTIL 499



 Score = 65.1 bits (157), Expect = 6e-15
 Identities = 52/221 (23%), Positives = 104/221 (47%), Gaps = 10/221 (4%)

Query: 275 ISLQLRQGEILGIYGLMGSGRSEFLNCIYGLTVADSGSVTLQGKPMPIGLPKATINAGMS 334
           + L LR GEI  + G  G+G+S  +  I G+   D+G+V+L G P+     +    AG++
Sbjct: 30  VDLTLRAGEIHALLGENGAGKSTLIKTITGVLRRDAGTVSLDGSPIAPHSAEEAATAGIA 89

Query: 335 LVTEDRKDSGLVLTGSILSNIALSAYKRLSSWSLINARKETQLAEDMVKR--LQIKTTSL 392
            V ++     L+   S+  N+ L   ++ + +  +   +  + A  +++   L I  T+ 
Sbjct: 90  TVYQE---VSLLPNLSVAQNLFLG--RQPTRFGFVREGETRRRARLLLRDFGLDIDVTA- 143

Query: 393 ELPVASMSGGNQQKVVLAKCLSTEPVCLLCDEPTRGIDEGAKQEIYHLLDQFVRGGGAAI 452
             P+ S S   +    +A+ +      L+ DEPT  +D    + ++ ++ +    G   +
Sbjct: 144 --PLDSYSVAVRHLTAIARAVDMSARVLILDEPTASLDANEVEILFTVMRKLAARGIGIV 201

Query: 453 VVSSEAPELLHLSDRIAVFKGGRLVTISTDTALSQEALLRL 493
            V+    ++  ++DRI V + GRLV       L +  L+R+
Sbjct: 202 FVTHFLDQVYAVTDRITVLRNGRLVDERLTAELPRMDLVRM 242


Lambda     K      H
   0.319    0.135    0.381 

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: 561
Number of extensions: 30
Number of successful extensions: 7
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: 495
Length of database: 510
Length adjustment: 34
Effective length of query: 461
Effective length of database: 476
Effective search space:   219436
Effective search space used:   219436
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 (21.8 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:

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 2024 update 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