Alignments for a candidate for iatA in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for iatA in Cupriavidus basilensis 4G11

Align Inositol transport ATP-binding protein IatA, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized)
to candidate RR42_RS32900 RR42_RS32900 sugar ABC transporter ATPase

Query= TCDB::B8H229
         (515 letters)



>FitnessBrowser__Cup4G11:RR42_RS32900
          Length = 502

 Score =  377 bits (969), Expect = e-109
 Identities = 221/496 (44%), Positives = 307/496 (61%), Gaps = 13/496 (2%)

Query: 3   LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62
           L ++  + K+FPGV+ALD V   +  GEVH LLGENGAGKS+L+K+L   + ADAG    
Sbjct: 10  LFEMRGICKNFPGVKALDDVSFAIYPGEVHMLLGENGAGKSSLMKVLCGVYVADAGEFYH 69

Query: 63  AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRL--GLVDWSRLRAD 120
            G  +    +P     LGIA I+QEF+L P L +A+N++LGREPR    G VD +R+ A+
Sbjct: 70  DGSPV-AITSPADTMGLGIAVIFQEFSLVPYLDIAQNIFLGREPRGRIPGSVDAARMHAE 128

Query: 121 AQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRLH 180
           A+ +L+ LG+ ++   PV  L VA+QQMVEIAKA++ NAR++++DEPTAALS RE ++L 
Sbjct: 129 ARRILDILGMEVSTRTPVHRLGVAQQQMVEIAKALSQNARILVLDEPTAALSDRETEKLF 188

Query: 181 AIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMVGRH 240
           A+IA LKA  VS+IY+SHR+ EV A+ DR T++RDGR V +    D    ++V  MVGR 
Sbjct: 189 AVIARLKADGVSMIYISHRMAEVFALGDRITILRDGRKVGACLPGDATPDELVARMVGRK 248

Query: 241 VEFE-RRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRT 299
           V+    R+R   PG V L V  V       SA   +  ++   R GEIVGLAGLVG+GR+
Sbjct: 249 VDMSYSRERSAQPGEVALDVRNV-------SADSGIADINLQVRAGEIVGLAGLVGSGRS 301

Query: 300 DLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLS 359
           ++AR +FGADPI  G + +  K L    P  A + G  L+PE RK +G  L  ++R NL 
Sbjct: 302 EVARAVFGADPIRQGEIYIFGKRL-TGGPDRARELGAALIPESRKSEGLALIRTVRDNLL 360

Query: 360 LPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMAL 419
           L  L+       +  ++AE  L E    +LRI   D       LSGGNQQK+++G+ +  
Sbjct: 361 LAGLRRAFPARWYRADKAEA-LAEREIARLRIATPDGNQLAQFLSGGNQQKIVIGKWLVA 419

Query: 420 TPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGV 479
             K+ I DEPTRGID+GAKAE+  ++  L   G  V++ISSEL E++ V DR  V R G 
Sbjct: 420 EAKLFIFDEPTRGIDVGAKAEIFALIDSLVKQGAGVLLISSELPEIINVCDRTYVMRGGR 479

Query: 480 IVADLDAQTATEEGLM 495
           I  ++     TEE ++
Sbjct: 480 IAGEVAHAEMTEERIL 495



 Score = 80.1 bits (196), Expect = 2e-19
 Identities = 68/250 (27%), Positives = 112/250 (44%), Gaps = 22/250 (8%)

Query: 256 VLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIAAGR 315
           + ++ G+    P + A   L  VSFA   GE+  L G  GAG++ L +++ G     AG 
Sbjct: 10  LFEMRGICKNFPGVKA---LDDVSFAIYPGEVHMLLGENGAGKSSLMKVLCGVYVADAGE 66

Query: 316 VLVDDKPLRLRSPRDAIQAGIM-------LVPEDRKQQGCFLDHSIRRNLSLPSLKALSA 368
              D  P+ + SP D +  GI        LVP     Q  FL    R  +      ++ A
Sbjct: 67  FYHDGSPVAITSPADTMGLGIAVIFQEFSLVPYLDIAQNIFLGREPRGRIP----GSVDA 122

Query: 369 LGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDE 428
                + R   D++               T + +L    QQ V + +A++   ++L++DE
Sbjct: 123 ARMHAEARRILDILGME--------VSTRTPVHRLGVAQQQMVEIAKALSQNARILVLDE 174

Query: 429 PTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQT 488
           PT  +      ++  V++ L   GV+++ IS  +AEV A+ DRI + R+G  V       
Sbjct: 175 PTAALSDRETEKLFAVIARLKADGVSMIYISHRMAEVFALGDRITILRDGRKVGACLPGD 234

Query: 489 ATEEGLMAYM 498
           AT + L+A M
Sbjct: 235 ATPDELVARM 244


Lambda     K      H
   0.320    0.136    0.380 

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: 704
Number of extensions: 37
Number of successful extensions: 10
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: 515
Length of database: 502
Length adjustment: 34
Effective length of query: 481
Effective length of database: 468
Effective search space:   225108
Effective search space used:   225108
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
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