GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Cupriavidus basilensis 4G11

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate RR42_RS32900 RR42_RS32900 sugar ABC transporter ATPase

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>FitnessBrowser__Cup4G11:RR42_RS32900
          Length = 502

 Score =  381 bits (979), Expect = e-110
 Identities = 227/508 (44%), Positives = 307/508 (60%), Gaps = 16/508 (3%)

Query: 12  PLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGEC 71
           PL  +R ICK FPGV+AL  V    Y GEVH L+GENGAGKS+LMK+L G Y AD  GE 
Sbjct: 9   PLFEMRGICKNFPGVKALDDVSFAIYPGEVHMLLGENGAGKSSLMKVLCGVYVAD-AGEF 67

Query: 72  HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRR--GLVARGDMVR 129
           + DG  V I  P     LG+AVI+QE SL P L +A+NI+LGR  + R  G V    M  
Sbjct: 68  YHDGSPVAITSPADTMGLGIAVIFQEFSLVPYLDIAQNIFLGREPRGRIPGSVDAARMHA 127

Query: 130 ACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRL 189
                L  LG + S    V  L +AQ+Q+VEIA+A+   ARILV+DEPT  LS  ET++L
Sbjct: 128 EARRILDILGMEVSTRTPVHRLGVAQQQMVEIAKALSQNARILVLDEPTAALSDRETEKL 187

Query: 190 FALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGR 249
           FA+I +L+ +G++++YISHRMAE+  L DR+T+LRDG  VG       +   LV  MVGR
Sbjct: 188 FAVIARLKADGVSMIYISHRMAEVFALGDRITILRDGRKVGACLPGDATPDELVARMVGR 247

Query: 250 DLSGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARL 309
            +   Y++    A   EV L VR+V+    +   +  +RAGE++GLAGLVG+GR+E+AR 
Sbjct: 248 KVDMSYSRER-SAQPGEVALDVRNVSADSGIADINLQVRAGEIVGLAGLVGSGRSEVARA 306

Query: 310 VFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHEN 369
           VFGAD   +GE+ I      G  +T   GGP +A + G A + E RK +GL L ++V +N
Sbjct: 307 VFGADPIRQGEIYI-----FGKRLT---GGPDRARELGAALIPESRKSEGLALIRTVRDN 358

Query: 370 INLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLL 429
           + L+   R A          A       I  L I           LSGGNQQK+++ + L
Sbjct: 359 L-LLAGLRRAFPARWYRADKAEALAEREIARLRIATPDGNQLAQFLSGGNQQKIVIGKWL 417

Query: 430 EIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMRE 489
             + ++ I DEPTRG+D+GAK+EI+ LI++L + G  +L+ISSELPE++ +CDR  VMR 
Sbjct: 418 VAEAKLFIFDEPTRGIDVGAKAEIFALIDSLVKQGAGVLLISSELPEIINVCDRTYVMRG 477

Query: 490 GTLAGEVRPAGSAAETQERIIALATGAA 517
           G +AGEV     A  T+ERI+ L    A
Sbjct: 478 GRIAGEV---AHAEMTEERILQLGMNDA 502


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: 700
Number of extensions: 45
Number of successful extensions: 11
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: 502
Length adjustment: 35
Effective length of query: 505
Effective length of database: 467
Effective search space:   235835
Effective search space used:   235835
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:

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