GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Pantoea rwandensis LMG 26275

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate WP_084934993.1 HA51_RS13475 sugar ABC transporter ATP-binding protein

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>NCBI__GCF_002095475.1:WP_084934993.1
          Length = 500

 Score =  374 bits (959), Expect = e-108
 Identities = 218/514 (42%), Positives = 323/514 (62%), Gaps = 22/514 (4%)

Query: 13  LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECH 72
           LL LR I K F  V+AL++V+LT  AGE+HAL GENGAGKSTLM I+ G    D  GE  
Sbjct: 4   LLELRGISKRFGAVKALQEVDLTLQAGEIHALAGENGAGKSTLMNIIDGILRPD-SGEIW 62

Query: 73  IDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRACA 132
           +DG+ V I  P+ A+ LG+ +++QE++L P++S+ ENI++  A Q+RGL+     +R  A
Sbjct: 63  LDGKPVTIRSPREAQQLGIGLVHQEIALCPDISIYENIWM--AHQQRGLLLPHKALRERA 120

Query: 133 PTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFAL 192
             +    A    +  V  LS++Q+QLVEIA+A+  + R+L++DEPT  L+  E   LF++
Sbjct: 121 QQVMNRLAPIPVSKKVGELSLSQQQLVEIAKALTLDCRLLILDEPTAALTEPEAQTLFSI 180

Query: 193 IRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDLS 252
           +RQLR +GM ++YISHRMAEI  L   +T+LRDG  V +   A ++   ++  +VGR+LS
Sbjct: 181 VRQLRDQGMTVVYISHRMAEIFALCQHITILRDGRTVHSAPLASMTADEVITRLVGRELS 240

Query: 253 GFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLVFG 312
             Y        +   +L VR+++DG+R     F+LR GE+LG+ GL+GAGR+E+A+ +  
Sbjct: 241 QLYPDKR-PVNDAPPLLEVRNISDGKRFHDIHFNLRPGEILGIGGLMGAGRSEIAQGICA 299

Query: 313 ADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENINL 372
               TRG +RI      G  V L       +I   + YL+EDRK  GLFL   +  NI+ 
Sbjct: 300 LQPLTRGSIRI-----KGEPVRLKDYAA--SIQQRMVYLSEDRKDAGLFLAMPIDWNIS- 351

Query: 373 IVAARDALGLGRLNRTAARRRTTEAIDTLG--IRVAHAQVN--VGALSGGNQQKVMLSRL 428
              A D   +     T + RR     + L   +++   +++  V +LSGGNQQKV L+R+
Sbjct: 352 ---ALDIRAVSHHGLTLSPRRERLQAEALAQQVKLKRGKLSDPVSSLSGGNQQKVALARV 408

Query: 429 LEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMR 488
           L +QP ++ LDEPTRGVD+ AK+EIY+++  LA +GV +++ISSELPE++GLCDR++V+ 
Sbjct: 409 LSVQPEIVFLDEPTRGVDVSAKAEIYQILANLAGNGVGLVVISSELPELIGLCDRIIVIH 468

Query: 489 EGTLAGEVRPAGSAAETQERIIALATGAAAAAPA 522
           EG ++GEV     AA T+E ++ LA G A  A A
Sbjct: 469 EGRISGEVT---GAAMTEENLMRLAAGIATQAEA 499


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: 622
Number of extensions: 25
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 540
Length of database: 500
Length adjustment: 35
Effective length of query: 505
Effective length of database: 465
Effective search space:   234825
Effective search space used:   234825
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:

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