Alignments for a candidate for iatA in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for iatA in Herbaspirillum seropedicae SmR1

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 HSERO_RS22220 HSERO_RS22220 D-ribose transporter ATP-binding protein

Query= TCDB::B8H229
         (515 letters)



>FitnessBrowser__HerbieS:HSERO_RS22220
          Length = 505

 Score =  370 bits (949), Expect = e-107
 Identities = 219/502 (43%), Positives = 310/502 (61%), Gaps = 20/502 (3%)

Query: 3   LLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADAGTVTF 62
           +L +S + K F GV AL  V   V  GEV ALLGENGAGKSTL+KIL+  H  D G++  
Sbjct: 12  VLSLSGIGKRFQGVVALQDVGFTVRPGEVMALLGENGAGKSTLVKILTGIHQPDEGSIHL 71

Query: 63  AGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREP-----RRLGLVDWSRL 117
            G+ +    A     + GI  ++QE  +F ELSVAEN+++GR+P     RR   +DW R+
Sbjct: 72  GGREVRFASAQ-DAMRGGITAVHQETVMFEELSVAENIWIGRQPLCGTPRR---IDWRRM 127

Query: 118 RADAQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVD 177
             +A+AL   L + L   A V+ L+VA++  VEIA+A++  A+++IMDEPTAALS  E+ 
Sbjct: 128 EDEARALFARLEVDLPVRARVKDLSVAQRHFVEIARALSQQAQVVIMDEPTAALSHHEIG 187

Query: 178 RLHAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVADMVRLMV 237
            L+ II  L+    +VI++SH+  E+ A+ DRYTV+RDGRF+ASG++AD+    +V LMV
Sbjct: 188 ELYRIIGQLRRAGTAVIFISHKFDEIYAVADRYTVLRDGRFIASGELADITEQQLVALMV 247

Query: 238 GRHV--EFER-RKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLV 294
           GR V   F R         A VL+V+        LS P     VSFA R GEI+G  GLV
Sbjct: 248 GREVGQVFSRAASNTEDQTAPVLEVK-------HLSHPSEFDDVSFAVRPGEILGFYGLV 300

Query: 295 GAGRTDLARLIFGADPIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSI 354
           GAGR+++   +FG  P A G V +D + ++L SP  AI  G+  VPEDR++QG  L   I
Sbjct: 301 GAGRSEVMHALFGLSPEAQGAVWIDGREVKLCSPAQAIAHGLAYVPEDRQRQGALLSLPI 360

Query: 355 RRNLSLPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLG 414
            +N++LP L  +    +    R E D+     ++L +K +     + +LSGGNQQKV+L 
Sbjct: 361 FQNITLPVLPGIGFFLR-RHRRREIDIARRLCEQLELKASHFHQHVAQLSGGNQQKVVLA 419

Query: 415 RAMALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVV 474
           + +A  P+VLI+DEPT+GIDIG+KA VH+ + +L   G+AV+++SSEL EVM +SDRIVV
Sbjct: 420 KWLATQPRVLILDEPTKGIDIGSKAAVHRFIGELVAQGLAVILVSSELPEVMGMSDRIVV 479

Query: 475 FREGVIVADLDAQTATEEGLMA 496
             +G +        A+ E L A
Sbjct: 480 MHQGRVQQVFSRAEASAEALAA 501



 Score = 91.7 bits (226), Expect = 6e-23
 Identities = 66/245 (26%), Positives = 118/245 (48%), Gaps = 8/245 (3%)

Query: 254 AVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAGRTDLARLIFGADPIAA 313
           A VL + G+     R      L+ V F  R GE++ L G  GAG++ L +++ G      
Sbjct: 10  APVLSLSGI---GKRFQGVVALQDVGFTVRPGEVMALLGENGAGKSTLVKILTGIHQPDE 66

Query: 314 GRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIRRNLSLPSLKALSALGQWV 373
           G + +  + +R  S +DA++ GI  V ++      F + S+  N+ +   + L    + +
Sbjct: 67  GSIHLGGREVRFASAQDAMRGGITAVHQETVM---FEELSVAENIWI-GRQPLCGTPRRI 122

Query: 374 DERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGRAMALTPKVLIVDEPTRGI 433
           D R   D       +L + +      +  LS   +  V + RA++   +V+I+DEPT  +
Sbjct: 123 DWRRMEDEARALFARLEVDLP-VRARVKDLSVAQRHFVEIARALSQQAQVVIMDEPTAAL 181

Query: 434 DIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVFREGVIVADLDAQTATEEG 493
                 E+++++  L   G AV+ IS +  E+ AV+DR  V R+G  +A  +    TE+ 
Sbjct: 182 SHHEIGELYRIIGQLRRAGTAVIFISHKFDEIYAVADRYTVLRDGRFIASGELADITEQQ 241

Query: 494 LMAYM 498
           L+A M
Sbjct: 242 LVALM 246


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: 644
Number of extensions: 28
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: 515
Length of database: 505
Length adjustment: 34
Effective length of query: 481
Effective length of database: 471
Effective search space:   226551
Effective search space used:   226551
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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Steps (tab-delimited)
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Protein sequences (fasta format)
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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