Alignments for a candidate for araG in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for araG in Pseudomonas simiae WCS417

Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate GFF2673 PS417_13635 D-ribose transporter ATP-binding protein

Query= CharProtDB::CH_014279
         (504 letters)



>FitnessBrowser__WCS417:GFF2673
          Length = 510

 Score =  363 bits (932), Expect = e-105
 Identities = 205/481 (42%), Positives = 300/481 (62%), Gaps = 7/481 (1%)

Query: 6   PYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNY-APTTGSV 64
           P L  +GI KTF G++ L  +    Y G++HALMGENGAGKSTL+KILSG Y A   G +
Sbjct: 5   PLLEMQGISKTFNGLRVLKTVGLKVYPGEIHALMGENGAGKSTLMKILSGAYQADPGGEI 64

Query: 65  VINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEA 124
            I GQ +   D   A   G+A+IYQEL L P ++VAENIYLG+   +G  ++R  +    
Sbjct: 65  RIAGQLIPTFDPATAKALGIAVIYQELSLCPNLSVAENIYLGRELRRGWTIDRKGMEAGC 124

Query: 125 GLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFR 184
              L+ LG +  P T +  LSI + Q+VEIA+AL  +AKI+  DEPT+ LS+RE D LF 
Sbjct: 125 IEVLQRLGAEFTPATRVSSLSIAERQLVEIARALHAHAKILVMDEPTTPLSSRETDRLFA 184

Query: 185 VIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRD 244
           +I++LR +G  I+Y+SHRM EI+ALSD ++V +DG Y+   T    +  +ALV+ MVGRD
Sbjct: 185 LIKQLRSQGLAIIYISHRMAEIYALSDRVSVLRDGHYIGELT-RDALSAEALVKMMVGRD 243

Query: 245 IGDIYGWQPRSY--GEERLRL-DAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKG 301
           +   Y  +  +Y  G   +R+ D      VR   S  + +GE++G+ GLVGAGR+EL + 
Sbjct: 244 LSGFYKKEHAAYNPGNVVMRVRDMADGKRVR-HCSFDLHAGEVLGIAGLVGAGRTELARL 302

Query: 302 MFGGTQITAGQVYIDQQPI-DIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISAR 360
           +F     T+G + +  + +  +R P+ AI AG++   EDRKA+G+    SV DNIN+ A 
Sbjct: 303 IFAADPRTSGTLEVVGKAVTPLRTPADAIRAGVVYLTEDRKAQGLFLDMSVADNINVCAC 362

Query: 361 RKHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKV 420
                 G V++       ++  I+SL+I+    +     LSGGNQQK +L R L  +  V
Sbjct: 363 VPDAHAGGVLDRDHALQRSNDAIKSLSIRVASGKVNAGALSGGNQQKVLLARLLEVKPHV 422

Query: 421 ILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGE 480
           ++LDEPTRG+D+G+K EIY +I  LA  G+ ++  SS+LPE++G  DR+++MREG++  E
Sbjct: 423 LILDEPTRGVDIGSKSEIYRIINQLAQAGIGIVVISSELPEIIGTCDRVLIMREGQLVAE 482

Query: 481 L 481
           +
Sbjct: 483 V 483



 Score = 77.4 bits (189), Expect = 1e-18
 Identities = 63/218 (28%), Positives = 102/218 (46%), Gaps = 22/218 (10%)

Query: 275 ISLAVRSGEIVGLFGLVGAGRSELMKGMFGGTQIT-AGQVYIDQQPIDIRKPSHAIAAG- 332
           + L V  GEI  L G  GAG+S LMK + G  Q    G++ I  Q I    P+ A A G 
Sbjct: 25  VGLKVYPGEIHALMGENGAGKSTLMKILSGAYQADPGGEIRIAGQLIPTFDPATAKALGI 84

Query: 333 ------MMLCPEDRKAEGIIPVHSVRDNINISARRKHVLGGCVINNGWEENNADHHIRSL 386
                 + LCP    AE I     +R    I   RK +  GC+             ++ L
Sbjct: 85  AVIYQELSLCPNLSVAENIYLGRELRRGWTID--RKGMEAGCI-----------EVLQRL 131

Query: 387 NIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVILLDEPTRGIDVGAKHEIYNVIYALA 446
             +   A + + +LS   +Q   + R L    K++++DEPT  +       ++ +I  L 
Sbjct: 132 GAEFTPATR-VSSLSIAERQLVEIARALHAHAKILVMDEPTTPLSSRETDRLFALIKQLR 190

Query: 447 AQGVAVLFASSDLPEVLGVADRIVVMREGEIAGELLHE 484
           +QG+A+++ S  + E+  ++DR+ V+R+G   GEL  +
Sbjct: 191 SQGLAIIYISHRMAEIYALSDRVSVLRDGHYIGELTRD 228


Lambda     K      H
   0.319    0.136    0.391 

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: 752
Number of extensions: 36
Number of successful extensions: 9
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: 504
Length of database: 510
Length adjustment: 34
Effective length of query: 470
Effective length of database: 476
Effective search space:   223720
Effective search space used:   223720
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 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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 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

GapMind for catabolism of small carbon sources