Alignments for a candidate for PS417_11890 in Cronobacter condimenti 1330

GapMind for catabolism of small carbon sources

Alignments for a candidate for PS417_11890 in Cronobacter condimenti 1330

Align Inositol transport system ATP-binding protein (characterized)
to candidate WP_007680679.1 BN137_RS01915 xylose ABC transporter ATP-binding protein

Query= reanno::WCS417:GFF2332
         (517 letters)



>NCBI__GCF_000319285.1:WP_007680679.1
          Length = 513

 Score =  400 bits (1028), Expect = e-116
 Identities = 229/506 (45%), Positives = 327/506 (64%), Gaps = 22/506 (4%)

Query: 21  PYLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDA--G 78
           PYLLE+ NI+K F  V A+ +V L + PG V++L GENG+GKSTLMK++ GIY   +  G
Sbjct: 2   PYLLEMKNITKAFGAVKAVDNVSLALAPGQVMSLCGENGSGKSTLMKVLCGIYPWGSYEG 61

Query: 79  EIRLRGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMH 138
           EI   G+P+        ++ GIA+IHQEL L+ ++++ ENI++G E +    ++++  M 
Sbjct: 62  EITFAGEPLTPTHIRDTERKGIAIIHQELALVKNLTVLENIFLGAE-ITRHGVLDYDAMT 120

Query: 139 RCTAELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAH 198
               +LLA++ + + P  + G+L + ++Q+VEIAKA++    +L++DEPT+++TE+E A 
Sbjct: 121 LRCEKLLAQVSLFVSPHTRTGDLGLGQQQLVEIAKALNKQVRLLVLDEPTASLTEQETAL 180

Query: 199 LFSIIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVG 258
           L  II DL+  G   +YI+HK+NEV AI+D + V RDG  I  + A  M+ + +I+MMVG
Sbjct: 181 LLDIIRDLQQHGIACIYISHKLNEVKAISDTICVIRDGKPISTRPAAQMSEEEIIAMMVG 240

Query: 259 RELSQLFPLRETPIGDLLLTVRDLT--------LDGVFKDVSFDLHAGEILGIAGLMGSG 310
           REL+ L+P      G+ +L V +LT        +  V   +SF L  GEILGIAGL+G+G
Sbjct: 241 RELTALYPSEPHSPGEEILRVENLTAWHPVNRHIQRV-SSLSFTLRRGEILGIAGLVGAG 299

Query: 311 RTNVAETIFGITPSS-SGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLE 369
           RT   + +FG+ P    G + +DG  V I     AI  G A++ EDRK  G+ P ++V +
Sbjct: 300 RTEAMQCLFGVWPGRWQGNVFIDGAPVTIRHCQQAIAHGIAMVPEDRKKDGIVPVMAVGQ 359

Query: 370 NMEMAVLPHYTGNGFIQQKALRALCEDMC-----KKLRVKTPSLEQCIDTLSGGNQQKAL 424
           N+ +A L  ++G       AL A  E  C     ++L+VKT S    I  LSGGNQQKA+
Sbjct: 360 NITLAALDQFSG----PLSALDAAAEQQCILDSLQRLKVKTASPMLAIGRLSGGNQQKAI 415

Query: 425 LARWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRV 484
           LAR L+ NPR+LILDEPTRGID+GAK EIY+LI  L  +G+AVI+ISSELPEVLG+SDRV
Sbjct: 416 LARCLLLNPRILILDEPTRGIDIGAKYEIYKLIHQLVQQGIAVIVISSELPEVLGLSDRV 475

Query: 485 MVMHEGELMGTLDRSEATQEKVMQLA 510
           +VMHEG L   L     TQE+VM+ A
Sbjct: 476 LVMHEGRLKANLINHNLTQEQVMEAA 501



 Score = 85.5 bits (210), Expect = 4e-21
 Identities = 65/232 (28%), Positives = 119/232 (51%), Gaps = 10/232 (4%)

Query: 290 DVSFDLHAGEILGIAGLMGSGRTNVAETIFGITP--SSSGQITLDGKAVRISDPHMAIEK 347
           +VS  L  G+++ + G  GSG++ + + + GI P  S  G+IT  G+ +  +       K
Sbjct: 22  NVSLALAPGQVMSLCGENGSGKSTLMKVLCGIYPWGSYEGEITFAGEPLTPTHIRDTERK 81

Query: 348 GFALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGNGFIQQKALRALCEDMCKKLRVKTPS 407
           G A++ ++     L   L+VLEN+ +      T +G +   A+   CE +  ++ +    
Sbjct: 82  GIAIIHQEL---ALVKNLTVLENIFLGA--EITRHGVLDYDAMTLRCEKLLAQVSLFVSP 136

Query: 408 LEQCIDTLSGGNQQKALLARWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMAV 467
             +  D L  G QQ   +A+ L    RLL+LDEPT  +     A +  +I  L   G+A 
Sbjct: 137 HTRTGD-LGLGQQQLVEIAKALNKQVRLLVLDEPTASLTEQETALLLDIIRDLQQHGIAC 195

Query: 468 IMISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKVMQLASG--MTAVH 517
           I IS +L EV  +SD + V+ +G+ + T   ++ ++E+++ +  G  +TA++
Sbjct: 196 IYISHKLNEVKAISDTICVIRDGKPISTRPAAQMSEEEIIAMMVGRELTALY 247


Lambda     K      H
   0.320    0.136    0.381 

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: 592
Number of extensions: 25
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: 517
Length of database: 513
Length adjustment: 35
Effective length of query: 482
Effective length of database: 478
Effective search space:   230396
Effective search space used:   230396
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:

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 2024 update 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