Aligments for a candidate for frcA in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Aligments for a candidate for frcA in Herbaspirillum seropedicae SmR1

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate HSERO_RS05195 HSERO_RS05195 xylose ABC transporter ATP-binding protein

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS05195 HSERO_RS05195 xylose ABC
           transporter ATP-binding protein
          Length = 518

 Score =  347 bits (889), Expect = e-100
 Identities = 213/512 (41%), Positives = 306/512 (59%), Gaps = 26/512 (5%)

Query: 13  LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYT-ADPGGEC 71
           +L +R I K+FPGV+AL  V L    GE+HA++GENGAGKSTLMK+LSG Y      G+ 
Sbjct: 4   ILEMRGIEKSFPGVKALNNVNLAVREGEIHAIVGENGAGKSTLMKVLSGVYPHGSYSGDI 63

Query: 72  HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRAC 131
              G+       + +  LG+ +I+QEL+L P LSV EN++LG    R G++         
Sbjct: 64  VYKGEVRAFKDIRDSEHLGIIIIHQELALVPLLSVMENLFLGNEQARGGVIDWEQSYVRA 123

Query: 132 APTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFA 191
              LA++G   SP   V  L + ++QL+EIA+A+  E ++L++DEPT  L+  ++D L  
Sbjct: 124 KELLAKVGLKESPLTQVGDLGVGKQQLIEIAKALSKEVKLLILDEPTASLNESDSDALLE 183

Query: 192 LIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLD-RAH-LSQAALVKMMVGR 249
           L+ +L+ +G+A + ISH++ EI ++AD +TVLRDG  V T D RA  +S+  +++ MVGR
Sbjct: 184 LLLELKRQGIASILISHKLNEISKVADSITVLRDGTTVDTFDCRAEPISEDRIIQHMVGR 243

Query: 250 DLSGFYTKTHGQAVEREVMLSVRDV-------ADGRRVKGCSFDLRAGEVLGLAGLVGAG 302
           +++  Y +   Q    EV+  VRD         D   +K  +  +RAGE++G+AGL+GAG
Sbjct: 244 EMADRYPQRDPQI--GEVIFEVRDWRVHHPLHTDRLAIKDVNMSVRAGEIVGIAGLMGAG 301

Query: 303 RTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFL 362
           RTELA+ +FG   R  G+         G  V L      +AI  GIAY+TEDRK  GL L
Sbjct: 302 RTELAKSIFG---RAYGKKITGQAFLHGKEVDLST--IEKAIAKGIAYVTEDRKGDGLVL 356

Query: 363 DQSVHENINLI----VAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGG 418
           ++ + +NI+L     V+ R  +   R  + AA  +       + IR +     V  LSGG
Sbjct: 357 EEDIKKNISLANLGGVSERTVIDEAREYKIAADFK-----QQMRIRCSSVLQKVVNLSGG 411

Query: 419 NQQKVMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVV 478
           NQQKV+LS+ L  QP VLILDEPTRG+D+GAK EIY +I+ LA  G  I+MISSE+PE++
Sbjct: 412 NQQKVVLSKWLFSQPEVLILDEPTRGIDVGAKFEIYNIISKLAAEGKCIIMISSEMPELL 471

Query: 479 GLCDRVLVMREGTLAGEVRPAGSAAETQERII 510
           G+CDR+ VM EG   G +  A +  E   R I
Sbjct: 472 GMCDRIYVMNEGQFVGHLPKAEATQENIMRAI 503



 Score = 81.3 bits (199), Expect = 8e-20
 Identities = 59/230 (25%), Positives = 113/230 (49%), Gaps = 13/230 (5%)

Query: 28  ALRKVELTAYAGEVHALMGENGAGKSTLMKILSG-AYTADPGGECHIDGQRVQIDGPQSA 86
           A++ V ++  AGE+  + G  GAG++ L K + G AY     G+  + G+ V +   + A
Sbjct: 278 AIKDVNMSVRAGEIVGIAGLMGAGRTELAKSIFGRAYGKKITGQAFLHGKEVDLSTIEKA 337

Query: 87  RDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRACAPTLARLGADF---- 142
              G+A + ++      L + E+I    +L   G V+   ++        ++ ADF    
Sbjct: 338 IAKGIAYVTEDRK-GDGLVLEEDIKKNISLANLGGVSERTVIDEAREY--KIAADFKQQM 394

Query: 143 -----SPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFALIRQLR 197
                S    V +LS   +Q V +++ +  +  +L++DEPT  +       ++ +I +L 
Sbjct: 395 RIRCSSVLQKVVNLSGGNQQKVVLSKWLFSQPEVLILDEPTRGIDVGAKFEIYNIISKLA 454

Query: 198 GEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMV 247
            EG  I+ IS  M E+  + DR+ V+ +G FVG L +A  +Q  +++ ++
Sbjct: 455 AEGKCIIMISSEMPELLGMCDRIYVMNEGQFVGHLPKAEATQENIMRAIM 504


Lambda     K      H
   0.320    0.136    0.382 

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: 604
Number of extensions: 24
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: 540
Length of database: 518
Length adjustment: 35
Effective length of query: 505
Effective length of database: 483
Effective search space:   243915
Effective search space used:   243915
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 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